Miscellaneous
17,439 items in 132 lists
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poliastro docs.poliastro.space
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Nautobot docs.nautobot.com
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The Haskell Tool Stack docs.haskellstack.org
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django-cms docs.django-cms.org
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doc2dash doc2dash.readthedocs.io
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discord.py discordpy.readthedocs.io
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Crest Ocean System crest.readthedocs.io
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CrateDB crate.io
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Argo CD argo-cd.readthedocs.io
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AiiDA demonstration aiida-qe-demo.readthedocs.io
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ZINC ligand discovery database zinc.docking.org
Free database of commercially-available compounds for virtual screening.
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WikiPathways wikipathways.org
Database of biological pathways.
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UniRef uniprot.org
Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds.
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UniProt REST API uniprot.org
Programmatic access to protein sequence and functional annotation data.
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UniProt uniprot.org
Functional information on proteins.
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Uniclust uniclust.mmseqs.com
Clustered protein sequence databases.
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Tox21 tripod.nih.gov
12,707 compounds tested in 12 nuclear receptor and stress-response pathway biochemical assays for toxicity prediction.
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BioGRID thebiogrid.org
Protein, genetic, and chemical interactions.
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ClinTox tdcommons.ai
Clinical toxicity dataset contrasting FDA-approved drugs with those that failed clinical trials due to toxicity.
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Therapeutics Data Commons (TDC) tdcommons.ai
Unified benchmark suite covering ADMET, drug-target interaction, drug response, and more.
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Tabula Sapiens tabula-sapiens-portal.ds.czbiohub.org
Comprehensive human single-cell atlas of ~500K cells from 24 organs and tissues across multiple donors.
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Tabula Muris tabula-muris.ds.czbiohub.org
Comprehensive single-cell atlas of 20 mouse organs and tissues, enabling cross-tissue and cross-species comparisons.
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STRING string-db.org
PPI networks for multiple organisms.
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STITCH stitch.embl.de
Chemical-protein interactions.
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Davis kinase inhibitors DB staff.cs.utu.fi
Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research.
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Squidpy squidpy.readthedocs.io
Python library for spatial single-cell analysis.
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SNAP snap.stanford.edu
Dataset of drug-gene interactions.
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Cancer Cell Line Encyclopedia sites.broadinstitute.org
Database of ~1000 cancer cell lines.
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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.
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SIGNOR 2.0 signor.uniroma2.it
Database of causal signaling interactions and pathways, with signed and directed relationships between proteins.
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SIDER (Side Effect Resource) sideeffects.embl.de
Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes.
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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.
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scvi-tools scvi-tools.org
Probabilistic models for single-cell omics data analysis.
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Scanpy scanpy.readthedocs.io
Python library for scRNA-seq analysis.
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Seurat satijalab.org
R library for scRNA-seq analysis.
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ROADMAP Epigenomics roadmapepigenomics.org
Reference epigenome maps for 111 primary human cell types and tissues, including histone modifications, chromatin accessibility, and DNA methylation.
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Rhea rhea-db.org
Database of chemical reactions.
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Rfam rfam.org
Database of RNA families with sequence alignments and consensus structures.
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Ensembl REST API rest.ensembl.org
API for genomic annotations, variants, genes, and comparative genomics.
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Drug Repurposing Hub repo-hub.broadinstitute.org
Collections of drug repurposing data (drug, MoA, target, etc).
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RegNetwork regnetworkweb.org
Database of gene regulatory networks covering transcription factor–target gene and miRNA–gene interaction data across multiple species.
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Reactome reactome.org
Expert-curated, peer-reviewed pathway database with detailed reaction mechanisms.
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PROTEIN DATA BANK (PDB) rcsb.org
3D structures of proteins, nucleic acids, complexes.
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PubChem pubchem.ncbi.nlm.nih.gov
One of the largest chemical databases (compounds, genes, and proteins).
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CPTAC (Clinical Proteomic Tumor Analysis Consortium) proteomics.cancer.gov
Multi-omic proteogenomic datasets for multiple cancer types linking proteomics with genomics.
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THE HUMAN PROTEIN ATLAS proteinatlas.org
Comprehensive human protein database (cells, tissues, organs).
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Critical Assessment of Structure Prediction (CASP) predictioncenter.org
Assessing methods for protein structure prediction.
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Cancer Therapeutics Response Portal (CTRP) portals.broadinstitute.org
Drug sensitivity profiles across ~900 cancer cell lines for >400 compounds.
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Replogle et al. 2022 K562 Genome-wide Perturb-seq plus.figshare.com
Genome-scale CRISPRi Perturb-seq targeting nearly all expressed genes in K562 cells.
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Open Targets Platform API platform.opentargets.org
API for target–disease associations integrating genetics, genomics, and drug data.
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