bioinformatics

rapids-singlecell: GPU-accelerated framework for scRNA analysis

🦒🦒🦒 Fool-proof, robust, and easy-to-use (robotic-UI-Research)🦒🦒🦒

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

Strelka2 germline and somatic small variant caller

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequen...

DANCE: a deep learning library and benchmark platform for single-cell analysis

Rapid large-scale prokaryote pan genome analysis

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

:microscope: BEDOPS: high-performance genomic feature operations

Tools for working with genomic and high throughput sequencing data.

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

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, an...

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

PyChem-Pro: 100% Python API, fast, flexible & programmable molecular viewer - 2D and 3D, molecular docking pose viewer, cheminformatics library, molec...

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Rapid comparison and dereplication of genomes

Single cell perturbation prediction

Successor of bwa-mem for short-read alignment

Application for making ENCODE Blacklists

Single-cell perturbation analysis

GenomeTools genome analysis system.

🧬 immunarch [R package] – Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Terminal protein structure viewer — interactive 3D visualization of PDB/mmCIF structures with cartoon ribbons, braille rendering, and Sixel/Kitty grap...

:microscope: Assemble large genomes using short reads

A unifying framework for biomedical research knowledge graphs

A curated list of awesome nanopore analysis tools.

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

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

Bayesian haplotype-based mutation calling

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

Python package with helper tools for the nf-core community.

Assembly and binning of metagenomes

Core BioPerl 1.x code

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

Modular and universal bioinformatics

Build a partitioned pangenome graph from microbial genomes

Proteomics search & quantification so fast that it feels like magic

parallel fastq-dump wrapper

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

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

SortMeRNA: next-generation sequence filtering and alignment tool

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

Inference of ploidy and heterozygosity structure using whole genome sequencing data