setuptools setuptools.pypa.io

nbsphinx nbsphinx.readthedocs.io

msticpy msticpy.readthedocs.io

Uberspace manual.uberspace.de

jupyter-book jupyterbook.org

jupyter-tutorial jupyter-tutorial.readthedocs.io

jupyter-sphinx jupyter-sphinx.readthedocs.io

Weblate docs.weblate.org

Wagtail docs.wagtail.org

SunPy docs.sunpy.org

Sidra Data Platform docs.sidra.dev

Scrapy docs.scrapy.org

Ray docs.ray.io

poliastro docs.poliastro.space

Nautobot docs.nautobot.com

The Haskell Tool Stack docs.haskellstack.org

django-cms docs.django-cms.org

doc2dash doc2dash.readthedocs.io

discord.py discordpy.readthedocs.io

Crest Ocean System crest.readthedocs.io

CrateDB crate.io

Argo CD argo-cd.readthedocs.io

AiiDA demonstration aiida-qe-demo.readthedocs.io

ZINC ligand discovery database zinc.docking.org

Free database of commercially-available compounds for virtual screening.

WikiPathways wikipathways.org

Database of biological pathways.

UniRef uniprot.org

Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds.

UniProt REST API uniprot.org

Programmatic access to protein sequence and functional annotation data.

UniProt uniprot.org

Functional information on proteins.

Uniclust uniclust.mmseqs.com

Clustered protein sequence databases.

Tox21 tripod.nih.gov

12,707 compounds tested in 12 nuclear receptor and stress-response pathway biochemical assays for toxicity prediction.

BioGRID thebiogrid.org

Protein, genetic, and chemical interactions.

ClinTox tdcommons.ai

Clinical toxicity dataset contrasting FDA-approved drugs with those that failed clinical trials due to toxicity.

Therapeutics Data Commons (TDC) tdcommons.ai

Unified benchmark suite covering ADMET, drug-target interaction, drug response, and more.

Tabula Sapiens tabula-sapiens-portal.ds.czbiohub.org

Comprehensive human single-cell atlas of ~500K cells from 24 organs and tissues across multiple donors.

Tabula Muris tabula-muris.ds.czbiohub.org

Comprehensive single-cell atlas of 20 mouse organs and tissues, enabling cross-tissue and cross-species comparisons.

STRING string-db.org

PPI networks for multiple organisms.

STITCH stitch.embl.de

Chemical-protein interactions.

Davis kinase inhibitors DB staff.cs.utu.fi

Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research.

Squidpy squidpy.readthedocs.io

Python library for spatial single-cell analysis.

SNAP snap.stanford.edu

Dataset of drug-gene interactions.

Cancer Cell Line Encyclopedia sites.broadinstitute.org

Database of ~1000 cancer cell lines.

Frangieh et al. 2021 Perturb-CITE-seq singlecell.broadinstitute.org

Multimodal CRISPR knockout screen with RNA and surface-protein readouts in patient-derived melanoma models under immune-related conditions.

SIGNOR 2.0 signor.uniroma2.it

Database of causal signaling interactions and pathways, with signed and directed relationships between proteins.

SIDER (Side Effect Resource) sideeffects.embl.de

Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes.

SeqBench seqbench.com

Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.

scvi-tools scvi-tools.org

Probabilistic models for single-cell omics data analysis.

Scanpy scanpy.readthedocs.io

Python library for scRNA-seq analysis.

Seurat satijalab.org

R library for scRNA-seq analysis.

ROADMAP Epigenomics roadmapepigenomics.org

Reference epigenome maps for 111 primary human cell types and tissues, including histone modifications, chromatin accessibility, and DNA methylation.

Rhea rhea-db.org

Database of chemical reactions.