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Genomics Libraries - Page 13

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ComBat-seqby zhangyuqing

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Batch effect adjustment based on negative binomial regression for RNA sequencing count data

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            muscatby HelenaLC

            R dotstar image 115 dotVersion:Currentdot
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            Multi-sample multi-group scRNA-seq analysis tools

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                      TPMCalculatorby ncbi

                      C++ dotstar image 115 dotVersion:Currentdot
                      License: Proprietary (Proprietary)

                      TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

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                                PoincareMapsby facebookresearch

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                                License: Proprietary (Proprietary)

                                The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

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                                          MISOby yarden

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                                          MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

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                                                    flotillaby YeoLab

                                                    Jupyter Notebook dotstar image 115 dotVersion:Currentdot
                                                    License: Permissive (BSD-3-Clause)

                                                    Reproducible machine learning analysis of gene expression and alternative splicing data

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                                                              matchmsby matchms

                                                              Python dotstar image 114 dotVersion:Currentdot
                                                              License: Permissive (Apache-2.0)

                                                              Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

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                                                                        sigminerby ShixiangWang

                                                                        R dotstar image 114 dotVersion:Currentdot
                                                                        License: Proprietary (Proprietary)

                                                                        🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

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                                                                                  graphtyperby DecodeGenetics

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                                                                                  Population-scale genotyping using pangenome graphs

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                                                                                            quickmergeby mahulchak

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                                                                                            License: Strong Copyleft (GPL-3.0)

                                                                                            A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

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                                                                                                      cgrangesby lh3

                                                                                                      C dotstar image 114 dotVersion:Currentdot
                                                                                                      License: Permissive (MIT)

                                                                                                      A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

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                                                                                                                BRANCHby baoe

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                                                                                                                Boosting RNA-Seq assemblies with partial or related genomic sequences

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                                                                                                                          itjh_3DTouchby itjhDev

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                                                                                                                          IT江湖 3D Touch Demo

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                                                                                                                                    interface-benchby teh-cmc

                                                                                                                                    Go dotstar image 114 dotVersion:Currentdot
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                                                                                                                                    [Go] interface-bench - a quick look at some of Go's subtleties regarding the use of interfaces.

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                                                                                                                                              IOBRby IOBR

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                                                                                                                                              License: Strong Copyleft (GPL-3.0)

                                                                                                                                              IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

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                                                                                                                                                        GENESPACEby jtlovell

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                                                                                                                                                        License: Proprietary (Proprietary)

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                                                                                                                                                                  NECATby xiaochuanle

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                                                                                                                                                                  Nanopore data assembler

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                                                                                                                                                                            seqsvrby nebula-chat

                                                                                                                                                                            C++ dotstar image 113 dotVersion:Currentdot
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                                                                                                                                                                            序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现

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                                                                                                                                                                                      htseqby simon-anders

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                                                                                                                                                                                      License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                      HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

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                                                                                                                                                                                                Scoaryby AdmiralenOla

                                                                                                                                                                                                Python dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                Pan-genome wide association studies

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                                                                                                                                                                                                          pybelby pybel

                                                                                                                                                                                                          Python dotstar image 112 dotVersion:Currentdot
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                                                                                                                                                                                                          🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

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                                                                                                                                                                                                                    pVACtoolsby griffithlab

                                                                                                                                                                                                                    Python dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                                    License: Permissive (BSD-3-Clause-Clear)

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                                                                                                                                                                                                                              srst2by katholt

                                                                                                                                                                                                                              Python dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                                              License: Proprietary (Proprietary)

                                                                                                                                                                                                                              Short Read Sequence Typing for Bacterial Pathogens

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                                                                                                                                                                                                                                        chip-seq-pipelineby ENCODE-DCC

                                                                                                                                                                                                                                        Python dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                                                        License: Permissive (MIT)

                                                                                                                                                                                                                                        ENCODE Uniform processing pipeline for ChIP-seq

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                                                                                                                                                                                                                                                  mixOmicsby mixOmicsTeam

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                                                                                                                                                                                                                                                  Development repository for the Bioconductor package 'mixOmics '

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                                                                                                                                                                                                                                                            gwas_scriptsby JoniColeman

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                                                                                                                                                                                                                                                            Codebook from my GWAS cookbook

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                                                                                                                                                                                                                                                                      rustling-ontologyby snipsco

                                                                                                                                                                                                                                                                      Rust dotstar image 112 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                      Ontology for rustling

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                                                                                                                                                                                                                                                                                biopiecesby maasha

                                                                                                                                                                                                                                                                                Perl dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                License: Strong Copyleft (GPL-2.0)

                                                                                                                                                                                                                                                                                Biopieces is a bioinformatic framework of tools easily used and easily created.

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                                                                                                                                                                                                                                                                                          ngsby ncbi

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                                                                                                                                                                                                                                                                                          NGS Language Bindings

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                                                                                                                                                                                                                                                                                                    gubbinsby nickjcroucher

                                                                                                                                                                                                                                                                                                    Python dotstar image 112 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                    License: Strong Copyleft (GPL-2.0)

                                                                                                                                                                                                                                                                                                    Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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                                                                                                                                                                                                                                                                                                              DNAnalyzerby VerisimilitudeX

                                                                                                                                                                                                                                                                                                              Java dotstar image 112 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                              Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

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                                                                                                                                                                                                                                                                                                                        qiitaby qiita-spots

                                                                                                                                                                                                                                                                                                                        Python dotstar image 111 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                        Qiita - A multi-omics databasing effort

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                                                                                                                                                                                                                                                                                                                                  vdjtoolsby mikessh

                                                                                                                                                                                                                                                                                                                                  Groovy dotstar image 111 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                                  Post-analysis of immune repertoire sequencing data

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                                                                                                                                                                                                                                                                                                                                            PRSiceby choishingwan

                                                                                                                                                                                                                                                                                                                                            C++ dotstar image 111 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                            License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                            A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

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                                                                                                                                                                                                                                                                                                                                                      gapseqby jotech

                                                                                                                                                                                                                                                                                                                                                      R dotstar image 111 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                      License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                                      Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

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                                                                                                                                                                                                                                                                                                                                                                svtyperby hall-lab

                                                                                                                                                                                                                                                                                                                                                                Python dotstar image 110 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                                                                                Bayesian genotyper for structural variants

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                                                                                                                                                                                                                                                                                                                                                                          canvasby Illumina

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                                                                                                                                                                                                                                                                                                                                                                          Canvas - Copy number variant (CNV) calling from DNA sequencing data

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                                                                                                                                                                                                                                                                                                                                                                                    SharpSearchby djhohnstein

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                                                                                                                                                                                                                                                                                                                                                                                    Search files for extensions as well as text within.

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                                                                                                                                                                                                                                                                                                                                                                                              tximportby mikelove

                                                                                                                                                                                                                                                                                                                                                                                              R dotstar image 110 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                                                                                              Import and summarize transcript-level estimates for gene-level analysis

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                                                                                                                                                                                                                                                                                                                                                                                                        Ranger-Mish-ImageWoof-5by lessw2020

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                                                                                                                                                                                                                                                                                                                                                                                                        Repo to build on / reproduce the record breaking Ranger-Mish-SelfAttention setup on FastAI ImageWoof dataset 5 epochs

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                                                                                                                                                                                                                                                                                                                                                                                                                  SCPby zhanghao-njmu

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                                                                                                                                                                                                                                                                                                                                                                                                                  License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                                                                                                  SCP provides a comprehensive set of tools for single cell data processing and downstream analysis.

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                                                                                                                                                                                                                                                                                                                                                                                                                            umisby vals

                                                                                                                                                                                                                                                                                                                                                                                                                            Python dotstar image 109 dotVersion:Currentdot
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                                                                                                                                                                                                                                                                                                                                                                                                                            Tools for processing UMI RNA-tag data

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                                                                                                                                                                                                                                                                                                                                                                                                                                      bioby dotnetbio

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                                                                                                                                                                                                                                                                                                                                                                                                                                      Bioinformatics library for .NET

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                                                                                                                                                                                                                                                                                                                                                                                                                                                omicsplaygroundby bigomics

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                                                                                                                                                                                                                                                                                                                                                                                                                                                Visual self-service analytics platform for big omics data.

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                                                                                                                                                                                                                                                                                                                                                                                                                                                          ExpansionHunterby Illumina

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                                                                                                                                                                                                                                                                                                                                                                                                                                                          A tool for estimating repeat sizes

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                    pancancerby greenelab

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Building classifiers using cancer transcriptomes across 33 different cancer-types

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              transvarby zwdzwd

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TransVar - multiway annotator for precision medicine

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        BGI-data-analysisby ehec-outbreak-crowdsourced

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Python dotstar image 108 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        no licences License: No License (No License)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        assemblies, annotations, further analysis on sequenced strains from the EHEC outbreak

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  i
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ipcaby bkelly-lab

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Python dotstar image 108 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  License: Permissive (MIT)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Instrumented Principal Components Analysis

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            VIBRANTby AnantharamanLab

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Python dotstar image 108 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Virus Identification By iteRative ANnoTation

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ComBat-seqby zhangyuqing
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Batch effect adjustment based on negative binomial regression for RNA sequencing count data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Rdotstar image 115dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                muscatby HelenaLC
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Multi-sample multi-group scRNA-seq analysis tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Rdotstar image 115dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TPMCalculatorby ncbi
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          C++dotstar image 115dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    PoincareMapsby facebookresearch
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    HTMLdotstar image 115dotUpdated: 4 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MISOby yarden
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Cdotstar image 115dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        flotillaby YeoLab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Reproducible machine learning analysis of gene expression and alternative splicing data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Jupyter Notebookdotstar image 115dotUpdated: 4 y agodot License: Permissive (BSD-3-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  m
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  matchmsby matchms
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pythondotstar image 114dotUpdated: 2 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            s
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            sigminerby ShixiangWang
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 114dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      g
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      graphtyperby DecodeGenetics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Population-scale genotyping using pangenome graphs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C++dotstar image 114dotUpdated: 3 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                q
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                quickmergeby mahulchak
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                C++dotstar image 114dotUpdated: 4 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          c
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          cgrangesby lh3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Cdotstar image 114dotUpdated: 4 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    B
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    BRANCHby baoe
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Boosting RNA-Seq assemblies with partial or related genomic sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    C++dotstar image 114dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              i
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              itjh_3DTouchby itjhDev
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              IT江湖 3D Touch Demo
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Swiftdotstar image 114dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        interface-benchby teh-cmc
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        [Go] interface-bench - a quick look at some of Go's subtleties regarding the use of interfaces.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Godotstar image 114dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  IOBRby IOBR
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Rdotstar image 114dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            GENESPACEby jtlovell
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 114dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      N
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      NECATby xiaochuanle
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Nanopore data assembler
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cdotstar image 113dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                seqsvrby nebula-chat
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                C++dotstar image 113dotUpdated: 4 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          h
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          htseqby simon-anders
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          C++dotstar image 113dotUpdated: 4 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Scoaryby AdmiralenOla
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pan-genome wide association studies
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pythondotstar image 112dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              pybelby pybel
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pythondotstar image 112dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        pVACtoolsby griffithlab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Pythondotstar image 112dotUpdated: 2 y agodot License: Permissive (BSD-3-Clause-Clear)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  s
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  srst2by katholt
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Short Read Sequence Typing for Bacterial Pathogens
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pythondotstar image 112dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            chip-seq-pipelineby ENCODE-DCC
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ENCODE Uniform processing pipeline for ChIP-seq
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pythondotstar image 112dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      mixOmicsby mixOmicsTeam
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Development repository for the Bioconductor package 'mixOmics '
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Rdotstar image 112dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                gwas_scriptsby JoniColeman
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Codebook from my GWAS cookbook
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Rdotstar image 112dotUpdated: 4 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          rustling-ontologyby snipsco
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Ontology for rustling
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rustdotstar image 112dotUpdated: 4 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    biopiecesby maasha
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Biopieces is a bioinformatic framework of tools easily used and easily created.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Perldotstar image 112dotUpdated: 4 y agodot License: Strong Copyleft (GPL-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ngsby ncbi
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              NGS Language Bindings
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              C++dotstar image 112dotUpdated: 3 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        gubbinsby nickjcroucher
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Pythondotstar image 112dotUpdated: 2 y agodot License: Strong Copyleft (GPL-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  DNAnalyzerby VerisimilitudeX
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Javadotstar image 112dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            qiitaby qiita-spots
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Qiita - A multi-omics databasing effort
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pythondotstar image 111dotUpdated: 2 y agodot License: Permissive (BSD-3-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      vdjtoolsby mikessh
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Post-analysis of immune repertoire sequencing data
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                PRSiceby choishingwan
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                C++dotstar image 111dotUpdated: 4 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          gapseqby jotech
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rdotstar image 111dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    svtyperby hall-lab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Bayesian genotyper for structural variants
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pythondotstar image 110dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              canvasby Illumina
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Canvas - Copy number variant (CNV) calling from DNA sequencing data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              C#dotstar image 110dotUpdated: 4 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SharpSearchby djhohnstein
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Search files for extensions as well as text within.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tximportby mikelove
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Import and summarize transcript-level estimates for gene-level analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Rdotstar image 110dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Ranger-Mish-ImageWoof-5by lessw2020
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Repo to build on / reproduce the record breaking Ranger-Mish-SelfAttention setup on FastAI ImageWoof dataset 5 epochs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Jupyter Notebookdotstar image 110dotUpdated: 4 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCPby zhanghao-njmu
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCP provides a comprehensive set of tools for single cell data processing and downstream analysis.
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                umisby vals
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Tools for processing UMI RNA-tag data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 109dotUpdated: 4 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          bioby dotnetbio
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Bioinformatics library for .NET
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          C#dotstar image 109dotUpdated: 4 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    omicsplaygroundby bigomics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Visual self-service analytics platform for big omics data.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Rdotstar image 109dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ExpansionHunterby Illumina
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              A tool for estimating repeat sizes
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