Most popular bioinformatics repositories and open source projects

pipeliner montilab Nextflow

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

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shinyChromosome YaoLab-Bioinfo R

an R/Shiny application for interactive creation of non-circular plots of whole genomes

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Afternotes Cinofix TeX

Afternotes for the attended courses at Ca' Foscari University, master in Data Management and Analytics.

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TwoPaCo medvedevgroup C++

A fast constructor of the compressed de Bruijn graph from many genomes

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tomahawk mklarqvist C++

Fast calculations of linkage-disequilibrium in large-scale human cohorts

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pyalign poke1024 C++

Fast and Versatile Alignments for Python

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shinyGEO jasdumas CSS

Gene Expression Omnibus Analysis with Shiny :microscope:

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clustergrammer2-notebooks ismms-himc Jupyter Notebook

Examples using Clustergrammer2 to explore high-dimensional datasets.

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pdb-benchmarks jgreener64 Python

Benchmarking common tasks on proteins in various languages and packages

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WormAnalysis gabyx Jupyter Notebook

Biological Engineering Test Code for Worm Analysis: https://stackoverflow.com/q/37820629/293195

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covtobed telatin C++

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

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panoptes cggh JavaScript

Eyes on your (genomic) data

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virtool virtool Python

Viral infection diagnostics using next-generation sequencing

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SINA epruesse C++

SINA - Reference based multiple sequence alignment

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dee2 markziemann Shell

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

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edge ginkgobioworks Python

Efficiently keep track of changes to genomes

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poreCov replikation Nextflow

SARS-CoV-2 workflow for nanopore sequence data

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TEsorter zhangrengang Pep8

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

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tcr imminfo R

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

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bionode-watermill bionode JavaScript

💧Bionode-Watermill: A (Not Yet Streaming) Workflow Engine

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BioCircos.R lvulliard JavaScript

Htmlwidgets binding R commands to the BioCircos.js library

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gonetics pbenner Go

Go / Golang Bioinformatics Library

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stochpy SystemsBioinformatics Python

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

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workflUX workflux JavaScript

An open-source, cloud-ready web application for simplified deployment of big data workflows.

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sketchy esteinig Rust

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

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bioseq-js lh3 HTML

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

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crimson bow Python

Bioinformatics tool outputs converter to JSON or YAML

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taxadb HadrienG Python

:hatching_chick: locally query the ncbi taxonomy

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Perl-for-Bioinformatics biocoder Python

An attempt to help anyone interested in using Perl for Bioinformatics

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oliver stjudecloud Python

An opinionated Cromwell orchestration manager.

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tiptoft andrewjpage Python

Predict plasmids from uncorrected long read data

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Wochenende MHH-RCUG Python

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

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NGS HorvathLab Python

Next-Gen Sequencing tools from the Horvath Lab

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OmicSelector kstawiski R

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic to...

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wdlRunR seandavi R

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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GeneticVariation.jl BioJulia Julia

Datastructures and algorithms for working with genetic variation

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psamm zhanglab Python

Curation and analysis of metabolic models

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grupo-estudo-bioinformatica pyladies-brazil Jupyter Notebook

Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.

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Skyhawk aquaskyline Python

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

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sbgnviz.js iVis-at-Bilkent JavaScript

A web based visualization tool for process description maps in SBGN

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2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF ucdavis-bioinformatics-training HTML

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

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partig lh3 C

An experimental tool to estimate the similarity between all pairs of contigs

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CuteVCF labsquare C++

simple viewer for variant call format using htslib

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BioPosDep datquocnguyen Python

Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)

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ctdna-pipeline OpenGene Shell

A simplified pipeline for ctDNA sequencing data analysis

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DCC dieterich-lab Python

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of f...

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