PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
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Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
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Download FASTQ files from SRA or ENA repositories.
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R toolkit for the analysis of single-cell chromatin data
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k-mer based assembly evaluation
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Detecting sites of genomic enrichment
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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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A UNIX-ey interface to OpenAI
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A Python API for the RCSB Protein Data Bank (PDB)
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HGVS variant name parsing and generation
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Simplified Data Exchange for HPC Simulations
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Source code for JBrowse 2, a modern React-based genome browser
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🍰 Hi, DIYgod
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software tools for haplotype assembly from sequence data
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Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
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Differential expression analysis for single-cell RNA-seq data.
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Simple Serilog log viewer UI for several sinks.
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pathfindR: Enrichment Analysis Utilizing Active Subnetworks
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FASTQ sequence quality visualisation with Emoji
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Python framework for Systems Biology modeling
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Various JavaScript lessons and code snippets.
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Quality control for MinION sequencing data
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Easy Amplicon data analysis pipeline
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haplotypic duplication identification tool
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Git Repository Analyzer.
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New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
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Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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File utilities designed for scalability and performance.
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Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
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Benchmarking of long-read assembly tools for bacterial whole genomes
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pymzML - an interface between Python and mzML Mass spectrometry Files
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Single-Cell Genotyping Tool
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Programs to analyse NGS data for population genetics purposes
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Automated, probabilistic assignment of cell types in scRNA-seq data
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RNA velocity estimation in Python
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Procedural macros to derive numeric traits in Rust
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Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
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INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
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Open Civic Data Division IDs definition & canonical repository
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ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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Accurate metagenomic profiling && Fast large-scale sequence/genome searching
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An R package for creating Q-Q and manhattan plots from GWAS results
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序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现
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A package to predict protein inter-residue geometries from sequence data
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WebAssembly modules for genomics
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ASCAT R package
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PopLDdecayby BGI-shenzhen
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
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nanofiltby wdecoster
Filtering and trimming of long read sequencing data
Python 150Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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Phinchby PitchInteractiveInc
Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
PHP 150Updated: 4 y ago License: Permissive (BSD-2-Clause)
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fastq-dlby rpetit3
Download FASTQ files from SRA or ENA repositories.
Python 150Updated: 2 y ago License: Permissive (MIT)
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signacby timoast
R toolkit for the analysis of single-cell chromatin data
R 150Updated: 3 y ago License: Proprietary (Proprietary)
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merquryby marbl
k-mer based assembly evaluation
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pindelby genome
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
C++ 150Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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openai_pipeby Aesthetikx
A UNIX-ey interface to OpenAI
Ruby 149Updated: 2 y ago License: Permissive (MIT)
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pypdbby williamgilpin
A Python API for the RCSB Protein Data Bank (PDB)
Python 148Updated: 3 y ago License: Permissive (MIT)
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hgvsby counsyl
HGVS variant name parsing and generation
Python 148Updated: 4 y ago License: Permissive (MIT)
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conduitby LLNL
Simplified Data Exchange for HPC Simulations
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jbrowse-componentsby GMOD
Source code for JBrowse 2, a modern React-based genome browser
TypeScript 147Updated: 2 y ago License: Permissive (Apache-2.0)
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HapCUT2by vibansal
software tools for haplotype assembly from sequence data
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Clair3by HKU-BAL
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Python 146Updated: 2 y ago
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p2rankby rdk
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
Groovy 145Updated: 1 y ago License: Permissive (MIT)
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diffxpyby theislab
Differential expression analysis for single-cell RNA-seq data.
Python 144Updated: 2 y ago License: Permissive (BSD-3-Clause)
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serilog-uiby mo-esmp
Simple Serilog log viewer UI for several sinks.
TypeScript 144Updated: 2 y ago License: Permissive (MIT)
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pathfindRby egeulgen
pathfindR: Enrichment Analysis Utilizing Active Subnetworks
R 144Updated: 2 y ago License: Proprietary (Proprietary)
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fastqeby fastqe
FASTQ sequence quality visualisation with Emoji
Python 143Updated: 4 y ago License: Permissive (BSD-3-Clause)
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pysbby pysb
Python framework for Systems Biology modeling
Python 142Updated: 2 y ago License: Permissive (BSD-2-Clause)
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JavaScript-Lessonsby buckyroberts
Various JavaScript lessons and code snippets.
JavaScript 142Updated: 4 y ago License: No License (No License)
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minion_qcby roblanf
Quality control for MinION sequencing data
R 142Updated: 4 y ago License: Permissive (MIT)
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EasyAmpliconby YongxinLiu
Easy Amplicon data analysis pipeline
HTML 142Updated: 2 y ago License: Proprietary (Proprietary)
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purge_dupsby dfguan
haplotypic duplication identification tool
C 141Updated: 2 y ago License: Permissive (MIT)
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gitstatsby evilsocket
Git Repository Analyzer.
Go 141Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
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NGBby epam
New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
Java 140Updated: 2 y ago License: Permissive (MIT)
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TOBIASby loosolab
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Python 140Updated: 2 y ago License: Permissive (MIT)
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xcmsby sneumann
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
R 140Updated: 2 y ago License: Proprietary (Proprietary)
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mpifileutilsby hpc
File utilities designed for scalability and performance.
C 140Updated: 1 y ago License: Permissive (BSD-3-Clause)
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protein-sequence-modelsby microsoft
Python 140Updated: 2 y ago License: Proprietary (Proprietary)
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gatk-protectedby broadgsa
Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
Java 139Updated: 4 y ago License: No License (No License)
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Long-read-assembler-comparisonby rrwick
Benchmarking of long-read assembly tools for bacterial whole genomes
Python 139Updated: 4 y ago License: Permissive (CC-BY-4.0)
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pymzMLby pymzml
pymzML - an interface between Python and mzML Mass spectrometry Files
Python 139Updated: 2 y ago License: Permissive (MIT)
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ngsToolsby mfumagalli
Programs to analyse NGS data for population genetics purposes
R 139Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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cellassignby Irrationone
Automated, probabilistic assignment of cell types in scRNA-seq data
R 139Updated: 3 y ago License: Proprietary (Proprietary)
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velocyto.pyby velocyto-team
RNA velocity estimation in Python
Python 138Updated: 2 y ago License: Permissive (BSD-2-Clause)
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num-deriveby rust-num
Procedural macros to derive numeric traits in Rust
Rust 138Updated: 1 y ago License: Permissive (Apache-2.0)
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ballgownby alyssafrazee
Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
R 138Updated: 2 y ago License: No License (No License)
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indraby sorgerlab
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Python 137Updated: 2 y ago License: Permissive (BSD-2-Clause)
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ocd-division-idsby opencivicdata
Open Civic Data Division IDs definition & canonical repository
Ruby 137Updated: 2 y ago License: Proprietary (Proprietary)
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ALLHiCby tangerzhang
ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
Perl 137Updated: 2 y ago License: No License (No License)
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kmcpby shenwei356
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Go 137Updated: 2 y ago License: Permissive (MIT)
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qqmanby stephenturner
An R package for creating Q-Q and manhattan plots from GWAS results
R 136Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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seqsvrby uidgen
序列号生成器－－《万亿级调用系统：微信序列号生成器架构设计及演变》开源实现
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trRosettaby gjoni
A package to predict protein inter-residue geometries from sequence data
Python 135Updated: 3 y ago License: Permissive (MIT)
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