Most popular bioinformatics repositories and open source projects

full_spectrum_bioinformatics

An open-access bioinformatics text

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dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets

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pyalign

Fast and Versatile Alignments for Python

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GECCO

GEne Cluster prediction with COnditional random fields.

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datasets-sars-cov-2

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/...

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GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in...

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TwoPaCo

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

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tomahawk

Fast calculations of linkage-disequilibrium in large-scale human cohor...

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xslt-sandbox

My xslt sandbox

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peptide-shaker

Interpretation of proteomics identification results

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enclone

VDJ Clonotyping & Analysis Tools

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shinyGEO

Gene Expression Omnibus Analysis with Shiny :microscope:

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SeqArray

Data management of large-scale whole-genome sequence variant calls (De...

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antigen.garnish

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metaspace

Cloud engine and platform for metabolite annotation for imaging mass s...

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bystro

Bystro genetic analysis (annotation, filtering, statistics)

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clustergrammer2-notebooks

Examples using Clustergrammer2 to explore high-dimensional datasets.

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pdb-benchmarks

Benchmarking common tasks on proteins in various languages and package...

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WormAnalysis

Biological Engineering Test Code for Worm Analysis: https://stackoverf...

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covtobed

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

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wiki

SciWiki: Collective KnowledgeBase for Scientific Data and Use

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orfipy

Fast and flexible ORF finder

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macrel

Predict AMPs in (meta)genomes and peptides

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empress

A fast and scalable phylogenetic tree viewer for microbiome data analy...

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MMseqs2-App

MMseqs2 app to run on your workstation or servers

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PATO

PATO is a R package designed to analyze pangenomes (set of genomes) in...

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pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

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BiG-SCAPE

Similarity networks of biosynthetic gene clusters

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BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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dnaio

Read and write FASTQ and FASTA efficiently from Python

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TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons...

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Scillus

R Package for Single-Cell Dataset Processing and Visualization

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fuc

Frequently used commands in bioinformatics

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IntaRNA

Efficient target prediction incorporating accessibility of interaction...

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stringMLST

Fast k-mer based tool for multi locus sequence typing (MLST)

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pypiper

Python toolkit for building restartable pipelines

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bindash

Fast and precise comparison of genomes and metagenomes (in the order o...

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virtool

Viral infection diagnostics using next-generation sequencing

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SINA

SINA - Reference based multiple sequence alignment

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dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly proces...

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IARC-nf

List of IARC bioinformatics nextflow pipelines

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edge

Efficiently keep track of changes to genomes

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TCC-GUI

📊 Graphical User Interface for TCC package

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isONclust

De novo clustering of long transcript reads into genes

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poreCov

SARS-CoV-2 workflow for nanopore sequence data

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tcr

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune...

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bionode-watermill

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

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BioCircos.R

Htmlwidgets binding R commands to the BioCircos.js library

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panoptes

Eyes on your (genomic) data

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gonetics

Go / Golang Bioinformatics Library

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