a python package for fast random access to sequences from plain and gzipped FASTA/Q files
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Simple simulation of single-cell RNA sequencing data
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Program for analysing NGS data.
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Bioconductor cheat sheet
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Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
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git clone --recursive on steroids
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EVcouplingsby debbiemarkslab
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177 Version:Current License: Proprietary (Proprietary)
Evolutionary couplings from protein and RNA sequence alignments
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CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
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TRAjectory-based Differential Expression analysis for SEQuencing data
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dN/dS methods to quantify selection in cancer and somatic evolution
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CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
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(Not Offical) BBMap short read aligner, and other bioinformatic tools.
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Viral genomics analysis pipelines
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List of gene lists for genomic analyses.
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Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
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Genome data visualizations
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Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
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Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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Source ontology files for the Gene Ontology
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DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
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SortMeRNA: next-generation sequence filtering and alignment tool
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starfish: unified pipelines for image-based transcriptomics
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The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
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A python extension for quick access to bigWig and bigBed files
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Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
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The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
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A PyTorch framework for prediction of tertiary protein structure
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a web application to apply/develop analysis tools for Molecular and Clinical data
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A collection of scripts and notes related to genomics and bioinformatics
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UGENE is free open-source cross-platform bioinformatics software
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Publication-quality sequence logos in R
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This repository contains OLD version of NArray. Please visit NEW version =>
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Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
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Spatial alignment of single cell transcriptomic data.
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A small database of weird gene annotations
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De novo genome assembler for long uncorrected reads
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gcp-for-bioinformaticsby lynnlangit
Jupyter Notebook 169 Version:Current License: Permissive (Apache-2.0)
GCP for Bioinformatics Researchers
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:pencil2: A versatile DNA sequence optimizer
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Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Nanopore sequence read simulator
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An ensemble approach to accurately detect somatic mutations using SomaticSeq
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Build a partitioned pangenome graph from microbial genomes
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Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
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make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
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Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
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My Sphinx Extensions
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Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
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pyfastxby lmdu
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
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splatterby Oshlack
Simple simulation of single-cell RNA sequencing data
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angsdby ANGSD
Program for analysing NGS data.
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bioc-refcardby mikelove
Bioconductor cheat sheet
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DRAMby WrightonLabCSU
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Python 178Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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verkkoby marbl
Python 178Updated: 1 y ago License: No License (No License)
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Giottoby drieslab
Spatial omics analysis toolbox
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git-fastcloneby square
git clone --recursive on steroids
Ruby 177Updated: 2 y ago License: Proprietary (Proprietary)
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EVcouplingsby debbiemarkslab
Evolutionary couplings from protein and RNA sequence alignments
Jupyter Notebook 177Updated: 2 y ago License: Proprietary (Proprietary)
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CellphoneDBby ventolab
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
Jupyter Notebook 177Updated: 2 y ago License: No License (No License)
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tradeSeqby statOmics
TRAjectory-based Differential Expression analysis for SEQuencing data
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dndscvby im3sanger
dN/dS methods to quantify selection in cancer and somatic evolution
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CellBenderby broadinstitute
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Python 174Updated: 1 y ago License: Permissive (BSD-3-Clause)
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BBMapby BioInfoTools
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
Java 174Updated: 2 y ago License: Proprietary (Proprietary)
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viral-ngsby broadinstitute
Viral genomics analysis pipelines
Python 174Updated: 2 y ago License: Proprietary (Proprietary)
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gene_listsby macarthur-lab
List of gene lists for genomic analyses.
Python 174Updated: 4 y ago License: No License (No License)
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leafcutterby davidaknowles
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
R 174Updated: 2 y ago License: Permissive (Apache-2.0)
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spacexrby dmcable
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
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AfterQCby OpenGene
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Python 173Updated: 4 y ago License: Permissive (MIT)
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nextcladeby nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
TypeScript 173Updated: 1 y ago License: Permissive (MIT)
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go-ontologyby geneontology
Source ontology files for the Gene Ontology
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deepconsensusby google
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Python 173Updated: 2 y ago License: Permissive (BSD-3-Clause)
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sortmernaby sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
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starfishby spacetx
starfish: unified pipelines for image-based transcriptomics
Python 172Updated: 3 y ago License: Permissive (MIT)
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pwizby ProteoWizard
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
C# 172Updated: 1 y ago License: Permissive (Apache-2.0)
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pyBigWigby deeptools
A python extension for quick access to bigWig and bigBed files
C 171Updated: 2 y ago License: Permissive (MIT)
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tabula-murisby czbiohub
Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
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KATby TGAC
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
C++ 171Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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openproteinby biolib
A PyTorch framework for prediction of tertiary protein structure
Python 170Updated: 2 y ago License: Permissive (MIT)
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Oncoscapeby FredHutch
a web application to apply/develop analysis tools for Molecular and Clinical data
JavaScript 170Updated: 4 y ago License: Permissive (MIT)
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genomicsby igordot
A collection of scripts and notes related to genomics and bioinformatics
R 170Updated: 2 y ago License: No License (No License)
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ugeneby ugeneunipro
UGENE is free open-source cross-platform bioinformatics software
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ggseqlogoby omarwagih
Publication-quality sequence logos in R
R 170Updated: 2 y ago License: No License (No License)
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narrayby masa16
This repository contains OLD version of NArray. Please visit NEW version =>
C 170Updated: 4 y ago License: No License (No License)
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lightdockby lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Python 170Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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Tangramby broadinstitute
Spatial alignment of single cell transcriptomic data.
Jupyter Notebook 170Updated: 1 y ago License: Permissive (BSD-3-Clause)
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oddgenesby cmdcolin
A small database of weird gene annotations
Perl 170Updated: 2 y ago License: No License (No License)
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ravenby lbcb-sci
De novo genome assembler for long uncorrected reads
C++ 169Updated: 2 y ago License: Permissive (MIT)
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gcp-for-bioinformaticsby lynnlangit
GCP for Bioinformatics Researchers
Jupyter Notebook 169Updated: 2 y ago License: Permissive (Apache-2.0)
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DnaChiselby Edinburgh-Genome-Foundry
:pencil2: A versatile DNA sequence optimizer
Python 168Updated: 1 y ago License: Permissive (MIT)
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megalodonby nanoporetech
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
Python 168Updated: 2 y ago License: Proprietary (Proprietary)
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NanoSimby bcgsc
Nanopore sequence read simulator
Python 168Updated: 2 y ago License: Proprietary (Proprietary)
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somaticseqby bioinform
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Python 167Updated: 2 y ago License: Permissive (BSD-2-Clause)
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PPanGGOLiNby labgem
Build a partitioned pangenome graph from microbial genomes
Python 166Updated: 1 y ago License: Proprietary (Proprietary)
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scCATCHby ZJUFanLab
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
R 166Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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EnrichedHeatmapby jokergoo
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
R 166Updated: 2 y ago License: Proprietary (Proprietary)
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WFAby smarco
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
C 165Updated: 3 y ago License: Proprietary (Proprietary)
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raconby lbcb-sci
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
C++ 164Updated: 1 y ago License: Permissive (MIT)
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