Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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Broad Institute Single Cell Portal singlecell.broadinstitute.org
Reducing barriers and accelerating single-cell research.
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Ensembl ensembl.org
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
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cBioPortal for Cancer Genomics cbioportal.org
Visualization, analysis and download of large-scale cancer genomics data sets.
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UK Biobank ukbiobank.ac.uk
A large-scale biomedical database and research resource with 500,000 research participants.
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Comparative Toxicogenomics Database ctdbase.org
paper - A database of manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. Useful for assembling ontologies of the related concepts, such as types of chemicals.
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Biopython biopython.org
paper - code - Python tools primarily intended for bioinformatics and computational molecular biology purposes, but also a convenient way to obtain data, including documents/abstracts from PubMed (see Chapter 9 of the documentation).
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ZINC ligand discovery database zinc.docking.org
Free database of commercially-available compounds for virtual screening.
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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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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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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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Davis kinase inhibitors DB staff.cs.utu.fi
Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research.
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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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