Most popular bioinformatics repositories and open source projects

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap...

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Deep_learning_examples

Examples of using deep learning in Bioinformatics

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single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA...

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minigraph

Proof-of-concept seq-to-graph mapper and graph generator

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RNAseq-workflow

A repository for setting up a RNAseq workflow

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cyvcf2

cython + htslib == fast VCF and BCF processing

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vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

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bioconvert

Bioconvert is a collaborative project to facilitate the interconversio...

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Bismark

A tool to map bisulfite converted sequence reads and determine cytosin...

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lightdock

Protein-protein, protein-peptide and protein-DNA docking framework bas...

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strelka

Strelka2 germline and somatic small variant caller

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bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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genometools

GenomeTools genome analysis system.

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raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

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plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covale...

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canvasXpress

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit...

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bionode

Modular and universal bioinformatics

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pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes:...

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AllenSDK

code for reading and processing Allen Institute for Brain Science data

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sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics too...

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homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package ma...

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octopus

Bayesian haplotype-based mutation calling

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Ribbon

A genome browser designed for complex structural variants and long rea...

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bioperl-live

Core BioPerl 1.x code

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awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases a...

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SURVIVOR

Toolset for SV simulation, comparison and filtering

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pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

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abyss

:microscope: Assemble large genomes using short reads

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bedops

:microscope: BEDOPS: high-performance genomic feature operations

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miniasm

Ultrafast de novo assembly for long noisy reads (though having no cons...

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serratus

Ultra-deep search for novel viruses

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bioSyntax

Syntax highlighting for computational biology

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Roary

Rapid large-scale prokaryote pan genome analysis

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mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation...

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GLUE

Graph-linked unified embedding for single-cell multi-omics data integr...

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karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along t...

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pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

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Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure f...

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intermine

A powerful open source data warehouse system

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histolab

Library for Digital Pathology Image Processing

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sarek

Analysis pipeline to detect germline or somatic variants (pre-processi...

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DeepECG

ECG classification programs based on ML/DL methods

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awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

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immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploratio...

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jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

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cellrank

CellRank: dynamics from multi-view single-cell data. See the docs:

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bowtie

An ultrafast memory-efficient short read aligner

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ugene

UGENE is free open-source cross-platform bioinformatics software

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janggu

Deep learning infrastructure for genomics

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