R package for the joint analysis of multiple single-cell RNA-seq datasets
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A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
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Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
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R package for analyzing single-cell RNA-seq data
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A tool set for short variant discovery in genetic sequence data.
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Algorithm for secondary de novo genome assembly guided by closely related references
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Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
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A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2
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VGP repository for the genome assembly working group
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SortMeRNA: next-generation sequence filtering and alignment tool
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Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
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R package for modeling single cell UMI expression data using regularized negative binomial regression
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Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
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Genomic Data Retrieval with R
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samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
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Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
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Rapid comparison and dereplication of genomes
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RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
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AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
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Creates github index for similar repositories discovery
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Supercomputing. Seamlessly. Open, Interactive HPC Via the Web
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a JavaScript DNA, RNA, and protein sequence viewer
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A cool place to store your Hi-C
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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
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A scanpy extension to analyse single-cell TCR and BCR data.
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A user-friendly workflow for phylogenomics
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RNA velocity estimation in R
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C++ 
158 Version:Current License: Proprietary (Proprietary)
A function that improves the default ADC reading accuracy to within 1%
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macromolecular crystallography library and utilities
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R package for DNA methylation analysis
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A package for including transposable elements in differential enrichment analysis of sequencing datasets.
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Inference of ploidy and heterozygosity structure using whole genome sequencing data
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Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
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ATAC-seq and DNase-seq processing pipeline
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A package to identify matched molecular pairs and use them to predict property changes.
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Full-Length Alternative Isoform analysis of RNA
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“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
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miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
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LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
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Lollipop-style mutation diagrams for annotating genetic variations.
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An openly-licensed corpus of small example files, covering a wide range of formats and creation tools.
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The nimble & robust variant annotator
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A template for data analysis projects structured as R packages (or not)
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structural variant calling and genotyping with existing tools, but, smoothly.
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Simulate genealogical trees and genomic sequence data using population genetic models
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Interpretation of T cell states using reference single-cell atlases
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conosby kharchenkolab
R package for the joint analysis of multiple single-cell RNA-seq datasets
R 164Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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pysamstatsby alimanfoo
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
Python 163Updated: 2 y ago
License: No License (No License)
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ssGSEA2.0by broadinstitute
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
R 163Updated: 2 y ago License: Proprietary (Proprietary)
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scdeby hms-dbmi
R package for analyzing single-cell RNA-seq data
R 163Updated: 2 y ago License: Proprietary (Proprietary)
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vtby atks
A tool set for short variant discovery in genetic sequence data.
C 163Updated: 4 y ago License: Permissive (MIT)
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AlignGraphby baoe
Algorithm for secondary de novo genome assembly guided by closely related references
C++ 163Updated: 4 y ago License: No License (No License)
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cNMFby dylkot
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Jupyter Notebook 163Updated: 1 y ago License: Permissive (MIT)
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InterVarby WGLab
A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
Python 162Updated: 1 y ago License: No License (No License)
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ggmsaby YuLab-SMU
:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2
R 162Updated: 2 y ago License: No License (No License)
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vgp-assemblyby VGP
VGP repository for the genome assembly working group
Shell 162Updated: 2 y ago License: Proprietary (Proprietary)
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sortmernaby biocore
SortMeRNA: next-generation sequence filtering and alignment tool
C++ 162Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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bifrostby pmelsted
Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
C++ 162Updated: 2 y ago License: Permissive (BSD-2-Clause)
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sctransformby satijalab
R package for modeling single cell UMI expression data using regularized negative binomial regression
R 162Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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Artemisby sanger-pathogens
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Java 161Updated: 3 y ago License: Proprietary (Proprietary)
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biomartrby ropensci
Genomic Data Retrieval with R
R 161Updated: 3 y ago License: No License (No License)
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samblasterby GregoryFaust
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
C++ 161Updated: 3 y ago License: Permissive (MIT)
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kingfisher-downloadby wwood
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
Python 161Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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drepby MrOlm
Rapid comparison and dereplication of genomes
Python 160Updated: 2 y ago License: No License (No License)
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RaGOOby malonge
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
Python 160Updated: 3 y ago License: Permissive (MIT)
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amrby ncbi
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
C++ 160Updated: 2 y ago License: Proprietary (Proprietary)
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throttlerby nozzle
Go 160Updated: 4 y ago License: Permissive (Apache-2.0)
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ghindexby anvaka
Creates github index for similar repositories discovery
JavaScript 159Updated: 3 y ago License: Permissive (MIT)
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ondemandby OSC
Supercomputing. Seamlessly. Open, Interactive HPC Via the Web
JavaScript 159Updated: 2 y ago License: Permissive (MIT)
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seqvizby Lattice-Automation
a JavaScript DNA, RNA, and protein sequence viewer
TypeScript 159Updated: 2 y ago License: Permissive (MIT)
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coolerby open2c
A cool place to store your Hi-C
Python 159Updated: 2 y ago License: Permissive (BSD-3-Clause)
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graphmapby isovic
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
C++ 159Updated: 4 y ago License: Permissive (MIT)
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scirpyby scverse
A scanpy extension to analyse single-cell TCR and BCR data.
Python 159Updated: 2 y ago License: Permissive (BSD-3-Clause)
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GToTreeby AstrobioMike
A user-friendly workflow for phylogenomics
Shell 158Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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velocyto.Rby velocyto-team
RNA velocity estimation in R
R 158Updated: 2 y ago License: No License (No License)
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ESP32-ADC-Accuracy-Improvement-functionby G6EJD
A function that improves the default ADC reading accuracy to within 1%
C++ 158Updated: 2 y ago License: Proprietary (Proprietary)
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gemmiby project-gemmi
macromolecular crystallography library and utilities
C++ 157Updated: 2 y ago License: Weak Copyleft (MPL-2.0)
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methylKitby al2na
R package for DNA methylation analysis
R 157Updated: 2 y ago License: No License (No License)
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TEtranscriptsby mhammell-laboratory
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
Python 156Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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js.mergeby yeikos
JavaScript 156Updated: 4 y ago License: Permissive (MIT)
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smudgeplotby KamilSJaron
Inference of ploidy and heterozygosity structure using whole genome sequencing data
R 156Updated: 2 y ago License: Permissive (Apache-2.0)
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Clairvoyanteby aquaskyline
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Python 155Updated: 4 y ago License: Permissive (BSD-3-Clause)
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atac_dnase_pipelinesby kundajelab
ATAC-seq and DNase-seq processing pipeline
Python 155Updated: 1 y ago License: Permissive (BSD-3-Clause)
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mmpdbby rdkit
A package to identify matched molecular pairs and use them to predict property changes.
Python 154Updated: 1 y ago License: Proprietary (Proprietary)
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flairby BrooksLabUCSC
Full-Length Alternative Isoform analysis of RNA
Python 154Updated: 2 y ago License: Proprietary (Proprietary)
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HiCPlotterby akdemirlab
“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
Python 154Updated: 2 y ago License: No License (No License)
154Updated: 2 y ago License: No License (No License)Support
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bio-playgroundby brentp
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
C 154Updated: 4 y ago License: Permissive (MIT)
154Updated: 4 y ago License: Permissive (MIT)Support
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LTR_retrieverby oushujun
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
Perl 153Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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lollipopsby joiningdata
Lollipop-style mutation diagrams for annotating genetic variations.
Go 153Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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format-corpusby openpreserve
An openly-licensed corpus of small example files, covering a wide range of formats and creation tools.
Java 152Updated: 2 y ago License: No License (No License)
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Nirvanaby Illumina
The nimble & robust variant annotator
C# 152Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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templateby Pakillo
A template for data analysis projects structured as R packages (or not)
R 152Updated: 2 y ago License: No License (No License)
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smooveby brentp
structural variant calling and genotyping with existing tools, but, smoothly.
Go 152Updated: 3 y ago License: Permissive (Apache-2.0)
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msprimeby tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
Python 151Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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copykatby navinlabcode
R 151Updated: 2 y ago License: No License (No License)
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ProjecTILsby carmonalab
Interpretation of T cell states using reference single-cell atlases
R 151Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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