awesome-computational-biology
Awesome list of computational biology.
https://github.com/inoue0426/awesome-computational-biology
Last synced: about 14 hours ago
JSON representation
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Databases
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scRNA
- Gene Expression Omnibus - Public functional genemics database.
- Single Cell PORTAL - Public database for single cell RNA.
- Single Cell Expression Atlas - Public database for single cell RNA.
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Compound
- PubChem - One of the biggest chemical database such as compounds, genes and proteins.
- ChEBI - Chemical database focused on small chemical compounds.
- ChEMBL - Database of bioactive molecules with drug-like properties.
- ChemSpider - Chemical structure database.
- KEGG COMPOUND - Collection of small molecules and biopolymers.
- LIPID MAPS - Database of lipids.
- Rhea - Database of chemical reactions.
- Drug Repurposing Hub - Collections of drug repurposing data containing drug, moa, target etc.
- Therapeutic Target Database - collections of drug-target, target-disease, and drug-disease dataset.
- ZINC ligand discovery database - Free database of commercially-available compounds for virtual screening.
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Pathway
- PathwayCommons - Database of Pathways and Interactions.
- KEGG PATHWAY - Collection fo drawn pathway maps.
- WikiPathways - Database of biological pathways.
- WikiPathways - Database of biological pathways.
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Mass Spectra
- MassBank - Open souce databases and tools for mass spectrometry reference spectra.
- MoNA MassBank of North America - Meta database of metabolite mass spectra, metadata and associated compounds.
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Protein
- THE HUMAN PROTEIN ATLAS - One of the biggest human protein database contained cells, tissues, and organs.
- PROTEIN DATA BANK - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.
- UniProt - The collection of functional information on proteins.
- AlphaFold Protein Structure Database - Database of 3D protein structures.
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Genome
- Human Genome Resources at NCBI - Database of image, proteomics, transcriptomics and systems biology.
- GenBank - Database of genetic sequence offered by NCBI.
- UCSC Genome Browser - Genome blowser offered by UCSC.
- cBioPortal - Database of Cancer Genomics. This has overall metaview for a lot of patients.
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Disease
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Interaction
- Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
- SNAP - A dataset which contains Drug-gene interactions.
- Comparative Toxicogenomics Database - A database for drug-target interactions.
- Therapeutics Data Commons - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.
- NCI60
- Genomics of Drug Sensitivity in Cancer (GDSC) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.
- Cancer Cell Line Encyclopedia - A database of cancer cell lines. This has 1000 cell lines.
- STITCH - A database of Chemical Protein Interaction.
- BindingDB - A database of compounds and targes.
- STRING - Protein-Protein Interaction Networks for several organisms.
- BioGRID - Database of Protein, Genetic and Chemical Interactions.
- HIPPIE - Human Protein-Protein Interaction database.
- Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
- HIPPIE - Human Protein-Protein Interaction database.
- Drug Mechanism Database (DrugMechDB)
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Preprocess
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Drug Response Prediction
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LLM for biology
- GeneGPT - LLM for biomedical information with several API.
- AI4Chem/ChemLLM-7B-Chat - LLM for chemical and molecule science
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API
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Interaction
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Programming Languages
Categories