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Genomics Libraries - Page 6

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MAESTROby liulab-dfci

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Single-cell Transcriptome and Regulome Analysis Pipeline

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            TCGAbiolinksby BioinformaticsFMRP

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            TCGAbiolinks

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                      gcassertby jordanlewis

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                      Assert your Go code is inlined and bounds-check eliminated

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                                signacby stuart-lab

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                                R toolkit for the analysis of single-cell chromatin data

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                                          bowtieby BenLangmead

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                                          An ultrafast memory-efficient short read aligner

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                                                    truvariby ACEnglish

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                                                    Structural variant toolkit for VCFs

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                                                              parallel-fastq-dumpby rvalieris

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                                                              parallel fastq-dump wrapper

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                                                                        scRepertoireby ncborcherding

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                                                                        A toolkit for single-cell immune profiling

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                                                                                  intermineby intermine

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                                                                                  A powerful open source data warehouse system

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                                                                                            SIPPYby CPCLAB-UNIPI

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                                                                                            Systems Identification Package for PYthon

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                                                                                                      Augustusby Gaius-Augustus

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                                                                                                      Genome annotation with AUGUSTUS

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                                                                                                                pcgrby sigven

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                                                                                                                Personal Cancer Genome Reporter (PCGR)

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                                                                                                                          kaijuby bioinformatics-centre

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                                                                                                                          Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

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                                                                                                                                    SingleRby dviraran

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                                                                                                                                    SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

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                                                                                                                                              ngmlrby philres

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                                                                                                                                              NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

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                                                                                                                                                        gridssby PapenfussLab

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                                                                                                                                                        GRIDSS: the Genomic Rearrangement IDentification Software Suite

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                                                                                                                                                                  whatshapby whatshap

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                                                                                                                                                                  Read-based phasing of genomic variants, also called haplotype assembly

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                                                                                                                                                                            sgaby jts

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                                                                                                                                                                            de novo sequence assembler using string graphs

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                                                                                                                                                                                      immunarchby immunomind

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                                                                                                                                                                                      🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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                                                                                                                                                                                                PyPoEby OmegaK2

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                                                                                                                                                                                                Collection of Python Tools for Path of Exile

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                                                                                                                                                                                                          danceby OmicsML

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                                                                                                                                                                                                          DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

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                                                                                                                                                                                                                    miniprotby lh3

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                                                                                                                                                                                                                    Align proteins to genomes with splicing and frameshift

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                                                                                                                                                                                                                              genomics_generalby simonhmartin

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                                                                                                                                                                                                                              General tools for genomic analyses.

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                                                                                                                                                                                                                                        cellrangerby 10XGenomics

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                                                                                                                                                                                                                                        10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

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                                                                                                                                                                                                                                                  DGE_workshopby hbctraining

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                                                                                                                                                                                                                                                            seurat-wrappersby satijalab

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                                                                                                                                                                                                                                                            Community-provided extensions to Seurat

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                                                                                                                                                                                                                                                                      Complete-Striped-Smith-Waterman-Libraryby mengyao

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                                                                                                                                                                                                                                                                                GEMMAby genetics-statistics

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                                                                                                                                                                                                                                                                                Genome-wide Efficient Mixed Model Association

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                                                                                                                                                                                                                                                                                          scanoramaby brianhie

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                                                                                                                                                                                                                                                                                          Panoramic stitching of single cell data

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                                                                                                                                                                                                                                                                                                    flowcraftby assemblerflow

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                                                                                                                                                                                                                                                                                                    FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

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                                                                                                                                                                                                                                                                                                              hgvsby biocommons

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                                                                                                                                                                                                                                                                                                              Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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                                                                                                                                                                                                                                                                                                                        vcfRby knausb

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                                                                                                                                                                                                                                                                                                                        Tools to work with variant call format files

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                                                                                                                                                                                                                                                                                                                                  giggleby ryanlayer

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                                                                                                                                                                                                                                                                                                                                  Interval data structure

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                                                                                                                                                                                                                                                                                                                                            KrakenToolsby jenniferlu717

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                                                                                                                                                                                                                                                                                                                                            KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

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                                                                                                                                                                                                                                                                                                                                                      NtSeqby keithwhor

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                                                                                                                                                                                                                                                                                                                                                      JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis.

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                                                                                                                                                                                                                                                                                                                                                                Blacklistby Boyle-Lab

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                                                                                                                                                                                                                                                                                                                                                                Application for making ENCODE Blacklists

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                                                                                                                                                                                                                                                                                                                                                                          centrifugeby DaehwanKimLab

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                                                                                                                                                                                                                                                                                                                                                                          Classifier for metagenomic sequences

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                                                                                                                                                                                                                                                                                                                                                                                    fgseaby ctlab

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                                                                                                                                                                                                                                                                                                                                                                                    Fast Gene Set Enrichment Analysis

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                                                                                                                                                                                                                                                                                                                                                                                              Kimera-Multiby MIT-SPARK

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                                                                                                                                                                                                                                                                                                                                                                                              Index repo for Kimera-Multi system

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                                                                                                                                                                                                                                                                                                                                                                                                        chip-seq-pipeline2by ENCODE-DCC

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                                                                                                                                                                                                                                                                                                                                                                                                        ENCODE ChIP-seq pipeline

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                                                                                                                                                                                                                                                                                                                                                                                                                  GraphAlignerby maickrau

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                                                                                                                                                                                                                                                                                                                                                                                                                            vcf2phylipby edgardomortiz

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                                                                                                                                                                                                                                                                                                                                                                                                                            Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

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                                                                                                                                                                                                                                                                                                                                                                                                                                      cell2locationby BayraktarLab

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                                                                                                                                                                                                                                                                                                                                                                                                                                      Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

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                                                                                                                                                                                                                                                                                                                                                                                                                                                pepperby kishwarshafin

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                                                                                                                                                                                                                                                                                                                                                                                                                                                PEPPER-Margin-DeepVariant

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                                                                                                                                                                                                                                                                                                                                                                                                                                                          MetaPhlAnby biobakery

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                                                                                                                                                                                                                                                                                                                                                                                                                                                          MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                    KMCby refresh-bio

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Fast and frugal disk based k-mer counter

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              oddtby oddt

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Open Drug Discovery Toolkit

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        LinuxKIby HewlettPackard

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        LinuxKI Toolset (Trace-based performance analysis tool)

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  mbeddr.coreby mbeddr

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Java dotstar image 201 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  License: Proprietary (Proprietary)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  The mbeddr core. An extensible C

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            GetOrganelleby Kinggerm

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Python dotstar image 201 dotVersion:Currentdot
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            License: Strong Copyleft (GPL-3.0)

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      MAESTROby liulab-dfci
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Single-cell Transcriptome and Regulome Analysis Pipeline
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cdotstar image 231dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCGAbiolinksby BioinformaticsFMRP
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCGAbiolinks
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Rdotstar image 231dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          gcassertby jordanlewis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Assert your Go code is inlined and bounds-check eliminated
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Godotstar image 230dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    signacby stuart-lab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    R toolkit for the analysis of single-cell chromatin data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Rdotstar image 227dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              bowtieby BenLangmead
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              An ultrafast memory-efficient short read aligner
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              C++dotstar image 225dotUpdated: 4 y agodot License: Weak Copyleft (Artistic-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        truvariby ACEnglish
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Structural variant toolkit for VCFs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Pythondotstar image 225dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  parallel-fastq-dumpby rvalieris
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  parallel fastq-dump wrapper
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pythondotstar image 224dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            scRepertoireby ncborcherding
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            A toolkit for single-cell immune profiling
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 224dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      intermineby intermine
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      A powerful open source data warehouse system
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Javadotstar image 223dotUpdated: 3 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SIPPYby CPCLAB-UNIPI
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Systems Identification Package for PYthon
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 223dotUpdated: 2 y agodot License: Weak Copyleft (LGPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Augustusby Gaius-Augustus
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Genome annotation with AUGUSTUS
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    pcgrby sigven
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Personal Cancer Genome Reporter (PCGR)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Rdotstar image 223dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              kaijuby bioinformatics-centre
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Cdotstar image 222dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SingleRby dviraran
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        HTMLdotstar image 222dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ngmlrby philres
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  C++dotstar image 222dotUpdated: 4 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            gridssby PapenfussLab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            GRIDSS: the Genomic Rearrangement IDentification Software Suite
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Javadotstar image 221dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      whatshapby whatshap
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Read-based phasing of genomic variants, also called haplotype assembly
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pythondotstar image 221dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                sgaby jts
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                de novo sequence assembler using string graphs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                C++dotstar image 221dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          immunarchby immunomind
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Rdotstar image 220dotUpdated: 2 y agodot License: Strong Copyleft (AGPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    PyPoEby OmegaK2
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Collection of Python Tools for Path of Exile
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pythondotstar image 219dotUpdated: 4 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              danceby OmicsML
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pythondotstar image 219dotUpdated: 2 y agodot License: Permissive (BSD-2-Clause)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        miniprotby lh3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Align proteins to genomes with splicing and frameshift
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Cdotstar image 218dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  genomics_generalby simonhmartin
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  General tools for genomic analyses.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pythondotstar image 217dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cellrangerby 10XGenomics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            10x Genomics Single Cell 3' Gene Expression and VDJ Assembly
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pythondotstar image 216dotUpdated: 2 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      DGE_workshopby hbctraining
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      HTMLdotstar image 216dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                seurat-wrappersby satijalab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Community-provided extensions to Seurat
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Rdotstar image 215dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Complete-Striped-Smith-Waterman-Libraryby mengyao
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Cdotstar image 214dotUpdated: 4 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    GEMMAby genetics-statistics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Genome-wide Efficient Mixed Model Association
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    C++dotstar image 213dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              scanoramaby brianhie
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Panoramic stitching of single cell data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pythondotstar image 212dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        flowcraftby assemblerflow
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Pythondotstar image 212dotUpdated: 4 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  hgvsby biocommons
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pythondotstar image 209dotUpdated: 2 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            vcfRby knausb
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Tools to work with variant call format files
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Rdotstar image 208dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      giggleby ryanlayer
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Interval data structure
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Cdotstar image 208dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                KrakenToolsby jenniferlu717
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 207dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          NtSeqby keithwhor
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          JavaScriptdotstar image 207dotUpdated: 5 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Blacklistby Boyle-Lab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Application for making ENCODE Blacklists
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    C++dotstar image 207dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              centrifugeby DaehwanKimLab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Classifier for metagenomic sequences
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              C++dotstar image 207dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        fgseaby ctlab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Fast Gene Set Enrichment Analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Rdotstar image 207dotUpdated: 4 y agodot License: Proprietary (Proprietary)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Kimera-Multiby MIT-SPARK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Index repo for Kimera-Multi system
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Shelldotstar image 207dotUpdated: 2 y agodotno licences License: No License (No License)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            chip-seq-pipeline2by ENCODE-DCC
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ENCODE ChIP-seq pipeline
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pythondotstar image 205dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GraphAlignerby maickrau
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C++dotstar image 205dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                vcf2phylipby edgardomortiz
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Pythondotstar image 204dotUpdated: 2 y agodot License: Strong Copyleft (GPL-3.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          cell2locationby BayraktarLab
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Pythondotstar image 204dotUpdated: 2 y agodot License: Permissive (Apache-2.0)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    pepperby kishwarshafin
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    PEPPER-Margin-DeepVariant
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pythondotstar image 203dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MetaPhlAnby biobakery
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pythondotstar image 203dotUpdated: 2 y agodot License: Permissive (MIT)
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        KMCby refresh-bio
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Fast and frugal disk based k-mer counter
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        C++dotstar image 203dotUpdated: 2 y agodotno licences License: No License (No License)
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