K-Dense-AI / scientific-agent-skills
A collection of 177 validated scientific skills for AI agents, covering biology, chemistry, medicine, and data analysis, plus 100+ scientific database references.
K-Dense-AI / scientific-agent-skills
mehek-builds / Entry-Level-Computational-Biology-Bioinformatics-Jobs
Title-screened computational biology, bioinformatics, biostatistics and biotech data science leads for early-career searches. Dated employer-board snapshots maintained by Litos.
thetahealth / mirobody
Turn scattered health data into answers you can trace. Self-hosted AI health data engine for lab reports, wearables and genetics, with a built-in MCP server. Run it with Docker and one LLM key, or keep every model local on llama.cpp.
biopython / biopython
Official git repository for Biopython (originally converted from CVS)
satijalab / seurat
R toolkit for single cell genomics
google / deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
soedinglab / MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
broadinstitute / gatk
Official code repository for GATK versions 4 and up
materialsproject / pymatgen
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
galaxyproject / galaxy
Data intensive science for everyone.
scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
vgteam / vg
tools for working with genome variation graphs
scikit-bio / scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
scverse / gget
🧬 gget enables efficient querying of genomic reference databases
ClawBio / ClawBio
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
cmdcolin / awesome-genome-visualization
A list of interesting genome browser and genome visualization programs
hail-is / hail
Cloud-native genomic dataframes and batch computing
cBioPortal / cbioportal
cBioPortal for Cancer Genomics
pysam-developers / pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
tanghaibao / goatools
Python library to handle Gene Ontology (GO) terms
BenLangmead / bowtie2
A fast and sensitive gapped read aligner
thackl / gggenomes
A grammar of graphics for comparative genomics
deeptools / deepTools
Tools to process and analyze deep sequencing data.
igvteam / igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
torognes / vsearch
Versatile open-source tool for microbiome analysis
igvteam / igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
ComparativeGenomicsToolkit / cactus
Official home of genome aligner based upon notion of Cactus graphs
vcflib / vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
oschwengers / bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
immunogenomics / harmony
Fast, sensitive and accurate integration of single-cell data with Harmony
genomoncology / biomcp
BioMCP: Biomedical Model Context Protocol
biojava / biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Ecogenomics / GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
scverse / squidpy
Spatial Single Cell Analysis in Python
oncologylab / fp-tools
Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports
Ensembl / ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
ncbi / datasets
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
sourmash-bio / sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
merenlab / anvio
An analysis and visualization platform for 'omics data
dellytools / delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
styczynski / bioseqdb
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
dportik / Biotech-Job-Search-Engine
A configurable, open-source job-discovery system for biotech, genomics, computational biology, bioinformatics, and adjacent life-science roles.
wrab12 / awesome-spatial-transcriptomics
A curated list of tools, foundation models, datasets and tutorials for spatial transcriptomics and single-cell analysis, ordered the way an analysis goes.
natera-open-source / vep-rs
A fast, memory-efficient variant effect predictor written in Rust: a from-scratch reimplementation of the Ensembl Variant Effect Predictor (VEP) that takes the same inputs and flags, emits VEP's consequence vocabulary in VEP's output formats, and annotates population-scale callsets two orders of magnitude faster than the Perl implementation.
raindrop668 / quantified-self-keto-protocol
A biohacking and metabolic debugging protocol for developers. Optimize fat loss & mental performance using genetic nutrigenomics.
jianshu93 / TurboANI
Homology-based ANI estimation at unprecedented scales🦀