A basecaller for Oxford Nanopore Technologies' sequencers
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A generative latent variable model for biological sequence families.
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kruschke-doing_bayesian_data_analysisby boboppie
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License: No License (No License)John K. Kruschke's Doing Bayesian Data Analysis: A Tutorial with R and BUGS
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A Bayesian model for compositional single-cell data analysis
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Proteomics search & quantification so fast that it feels like magic
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SquiggleKit: A toolkit for manipulating nanopore signal data
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A Serilog sink that writes events to the Seq structured log server
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Reference-guided transcript discovery and quantification for long read RNA-Seq data
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Fast Principal Component Analysis of Large-Scale Genome-Wide Data
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Similar genome assisted reassembly pipeline for PacBio long reads
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A modular, python-based framework for mass spectrometry. Powered by nbdev.
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AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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V-pipe is a pipeline designed for analysing NGS data of short viral genomes
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:microscope::books: Galaxy Tool wrappers
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🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
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A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
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Rapid Profiling and Deconvolution Tool for Metagenomes
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An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
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AddOn for Blender to do molecular work
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A fork of the original cvs based IKVM repository
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Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
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This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset
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Analysis pipeline for cancer sequencing data
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genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
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Haplotype-aware CNV analysis from single-cell RNA-seq
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A scalable SCENIC workflow for single-cell gene regulatory network analysis
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A cool place to store your Hi-C
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Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
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:floppy_disk: C++ & Python API for Scientific I/O
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Base Classes and Functions for Mass Spectrometry and Proteomics
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an R/shiny application for creation of Circos plot interactively
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microsatellite instability detection using tumor only or paired tumor-normal data
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Sequana: a set of Snakemake NGS pipelines
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MOLGENIS - for scientific data: management, exploration, integration and analysis.
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Tools for manipulating biological data, particularly multiple sequence alignments
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A project to extract CRISPR information from open genetic data.
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Long read based human genomic structural variation detection with cuteSV
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GeoCAT-comp provides implementations of computational functions for operating on geosciences data. Many of these functions originated in NCL and were translated into Python.
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MyGene.info: A BioThings API for gene annotations
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We've moved! Please use the new repository 🠊 https://github.com/enketo/enketo-express
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Gene fusion detection and visualization
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Curated Metagenomic Data of the Human Microbiome
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Interfaces for HDF5-based Single Cell File Formats
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Deep-learning Augmented RNA-seq analysis of Transcript Splicing
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NGS-pipe: next-generation sequencing pipelines for precision oncology
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Application for inferring subclonal composition and evolution from whole-genome sequencing data.
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PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
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Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
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Genomics Extension for SQLite
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Chironby haotianteng
A basecaller for Oxford Nanopore Technologies' sequencers
Python 108Updated: 3 y ago License: Proprietary (Proprietary)
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DeepSequenceby debbiemarkslab
A generative latent variable model for biological sequence families.
Python 108Updated: 4 y ago License: Permissive (MIT)
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kruschke-doing_bayesian_data_analysisby boboppie
John K. Kruschke's Doing Bayesian Data Analysis: A Tutorial with R and BUGS
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scCODAby theislab
A Bayesian model for compositional single-cell data analysis
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sageby lazear
Proteomics search & quantification so fast that it feels like magic
Rust 108Updated: 2 y ago License: Permissive (MIT)
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SquiggleKitby Psy-Fer
SquiggleKit: A toolkit for manipulating nanopore signal data
Python 107Updated: 2 y ago License: Permissive (MIT)
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serilog-sinks-seqby serilog
A Serilog sink that writes events to the Seq structured log server
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bambuby GoekeLab
Reference-guided transcript discovery and quantification for long read RNA-Seq data
R 107Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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flashpcaby gabraham
Fast Principal Component Analysis of Large-Scale Genome-Wide Data
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AlignGraph2by Godotcoffee
Similar genome assisted reassembly pipeline for PacBio long reads
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alphapeptby MannLabs
A modular, python-based framework for mass spectrometry. Powered by nbdev.
Python 107Updated: 3 y ago License: Permissive (Apache-2.0)
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AmpliconArchitectby virajbdeshpande
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
Python 106Updated: 2 y ago License: No License (No License)
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V-pipeby cbg-ethz
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
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galaxytoolsby bgruening
:microscope::books: Galaxy Tool wrappers
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alevin-fryby COMBINE-lab
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Rust 106Updated: 2 y ago License: Permissive (BSD-3-Clause)
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bedtkby lh3
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
C 106Updated: 4 y ago License: Permissive (MIT)
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RaPDToolby ayixon
Rapid Profiling and Deconvolution Tool for Metagenomes
Python 106Updated: 3 y ago License: Permissive (MIT)
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atroposby jdidion
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Python 105Updated: 4 y ago License: Proprietary (Proprietary)
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PhyloSuiteby dongzhang0725
PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
Python 105Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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BioBlenderby MonZop
AddOn for Blender to do molecular work
Python 105Updated: 4 y ago License: Permissive (BSD-2-Clause)
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ikvm-forkby mono
A fork of the original cvs based IKVM repository
C# 105Updated: 4 y ago License: Proprietary (Proprietary)
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BuddySuiteby biologyguy
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Python 105Updated: 3 y ago License: Proprietary (Proprietary)
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scell_lung_adenocarcinomaby czbiohub
This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset
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superFreqby ChristofferFlensburg
Analysis pipeline for cancer sequencing data
R 105Updated: 2 y ago License: Permissive (MIT)
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peddyby brentp
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Jupyter Notebook 105Updated: 4 y ago License: Permissive (MIT)
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numbatby kharchenkolab
Haplotype-aware CNV analysis from single-cell RNA-seq
R 105Updated: 2 y ago License: Proprietary (Proprietary)
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SCENICprotocolby aertslab
A scalable SCENIC workflow for single-cell gene regulatory network analysis
Python 104Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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coolerby mirnylab
A cool place to store your Hi-C
Python 104Updated: 5 y ago License: Permissive (BSD-3-Clause)
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PORPOISEby mahmoodlab
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
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openPMD-apiby openPMD
:floppy_disk: C++ & Python API for Scientific I/O
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MSnbaseby lgatto
Base Classes and Functions for Mass Spectrometry and Proteomics
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shinyCircosby venyao
an R/shiny application for creation of Circos plot interactively
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msisensorby ding-lab
microsatellite instability detection using tumor only or paired tumor-normal data
C++ 104Updated: 4 y ago License: Permissive (MIT)
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sequanaby sequana
Sequana: a set of Snakemake NGS pipelines
Jupyter Notebook 104Updated: 4 y ago License: Permissive (BSD-3-Clause)
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molgenisby molgenis
MOLGENIS - for scientific data: management, exploration, integration and analysis.
Java 103Updated: 2 y ago License: Weak Copyleft (LGPL-3.0)
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bx-pythonby bxlab
Tools for manipulating biological data, particularly multiple sequence alignments
Python 103Updated: 4 y ago License: Permissive (MIT)
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phageParserby phageParser
A project to extract CRISPR information from open genetic data.
Python 103Updated: 4 y ago License: Permissive (MIT)
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cuteSVby tjiangHIT
Long read based human genomic structural variation detection with cuteSV
Python 102Updated: 3 y ago License: Permissive (MIT)
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geocat-compby NCAR
GeoCAT-comp provides implementations of computational functions for operating on geosciences data. Many of these functions originated in NCL and were translated into Python.
Python 102Updated: 2 y ago License: Permissive (Apache-2.0)
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mygene.infoby biothings
MyGene.info: A BioThings API for gene annotations
Python 102Updated: 2 y ago License: Proprietary (Proprietary)
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enketo-expressby kobotoolbox
We've moved! Please use the new repository 🠊 https://github.com/enketo/enketo-express
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GeneFuseby OpenGene
Gene fusion detection and visualization
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curatedMetagenomicDataby waldronlab
Curated Metagenomic Data of the Human Microbiome
R 102Updated: 2 y ago License: Weak Copyleft (Artistic-2.0)
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seurat-diskby mojaveazure
Interfaces for HDF5-based Single Cell File Formats
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DARTSby Xinglab
Deep-learning Augmented RNA-seq analysis of Transcript Splicing
Python 101Updated: 2 y ago License: Proprietary (Proprietary)
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NGS-pipeby cbg-ethz
NGS-pipe: next-generation sequencing pipelines for precision oncology
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phylowgsby morrislab
Application for inferring subclonal composition and evolution from whole-genome sequencing data.
Python 101Updated: 2 y ago License: Strong Copyleft (GPL-3.0)
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PhysiCellby MathCancer
PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
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powsimRby bvieth
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
R 101Updated: 2 y ago License: Weak Copyleft (Artistic-2.0)
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GenomicSQLiteby mlin
Genomics Extension for SQLite
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