bioinformatics
Repositories (1438)
Scikit-learn compatible library for molecular fingerprints and chemoinformatics
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequen...
A curated and summarized list of bioinformatics bench-marking papers and resources.
rapids-singlecell: GPU-accelerated framework for scRNA analysis
AI-Powered Bioinformatics Research Assistant. Built on OpenClaw.
Package for fetching metadata and downloading data from SRA/ENA/GEO
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Single cell perturbation prediction
🧬 immunarch [R package] – Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design
Application for making ENCODE Blacklists
Rapid comparison and dereplication of genomes
GenomeTools genome analysis system.
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
:microscope: Assemble large genomes using short reads
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
Bayesian haplotype-based mutation calling
Core BioPerl 1.x code
Modular and universal bioinformatics
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
A curated list of awesome nanopore analysis tools.
parallel fastq-dump wrapper
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Python package with helper tools for the nf-core community.
A genome browser designed for complex structural variants and long reads.
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
A unifying framework for biomedical research knowledge graphs
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
Build a partitioned pangenome graph from microbial genomes
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Inference of ploidy and heterozygosity structure using whole genome sequencing data
GCP for Bioinformatics Researchers
SortMeRNA: next-generation sequence filtering and alignment tool
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
Assembly and binning of metagenomes
Proteomics search & quantification so fast that it feels like magic
Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).
Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.
minimal example implementations for bioinformatics workflow managers
Reads simulator
Source code for JBrowse 2, a modern React-based genome browser
ECG classification programs based on ML/DL methods
Finds SNP sites from a multi-FASTA alignment file
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling asses...
Versatile computational pipeline for processing protein structure data for deep learning applications.
Ultra-deep search for novel viruses