Miscellaneous
17,439 items in 132 lists
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Open Targets Platform platform.opentargets.org
Systematic target identification and prioritization platform integrating genetics, genomics, and drug data for drug discovery.
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PK-DB pk-db.com
Open database of experimental pharmacokinetics (PK) and ADME data from clinical and preclinical studies.
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PharmGKB pharmgkb.org
Curated pharmacogenomics dataset linking genetic variants to drug response phenotypes across thousands of drugs.
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PDBBind pdbbind-plus.org.cn
Binding affinity data for biomolecular complexes.
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PathwayCommons pathwaycommons.org
Database of pathways and interactions.
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kallisto pachterlab.github.io
Near-optimal RNA-seq quantification using pseudoalignment for fast transcript abundance estimation.
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SAbDab opig.stats.ox.ac.uk
Structural Antibody Database containing all antibody structures in the PDB.
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OADB (Observed Antibody Space Database) opig.stats.ox.ac.uk
Database of antibody sequences from immune repertoire sequencing.
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OncoKB oncokb.org
Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
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OmniPath omnipathdb.org
Comprehensive resource integrating protein interactions, signaling pathways, gene regulatory networks, and miRNA targets from over 100 databases.
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OMIM (Online Mendelian Inheritance in Man) omim.org
Comprehensive database of human genes and genetic disorders.
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OGB (Open Graph Benchmark) ogb.stanford.edu
Large-scale graph ML benchmark suite including biological datasets such as ogbl-ppa (protein-protein associations) and ogbg-molhiv.
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PubMed E-utilities (esearch/efetch) nlm.nih.gov
APIs for searching and retrieving biomedical literature from PubMed.
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NeXtProt nextprot.org
Expert knowledge base on human proteins with deep functional annotation, complementary to UniProt.
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Human Genome Resources at NCBI ncbi.nlm.nih.gov
Database for genomics, proteomics, transcriptomics, and systems biology.
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Datlinger et al. 2017 CROP-seq ncbi.nlm.nih.gov
Pooled CRISPR knockout screen with single-cell transcriptomic readout in Jurkat cells under T-cell receptor stimulation.
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Adamson et al. 2016 Perturb-seq ncbi.nlm.nih.gov
CRISPRi Perturb-seq in K562 cells for systematic dissection of the unfolded protein response.
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Dixit et al. 2016 Perturb-seq ncbi.nlm.nih.gov
Pooled CRISPR knockout with single-cell RNA-seq across K562 and dendritic-cell screens, including stimulated conditions and combinatorial perturbations.
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GSE191127 Breast Cancer Pre/Post Chemotherapy ncbi.nlm.nih.gov
Bulk RNA-seq and genomics from matched pre- and post-neoadjuvant chemotherapy breast tumors with treatment outcomes.
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sci-Plex ncbi.nlm.nih.gov
Single-cell chemical perturbation screen of ~650,000 transcriptomes across three cancer cell lines, 188 compounds, and four doses.
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Gasperini et al. 2019 CRISPRi enhancer screen ncbi.nlm.nih.gov
High-MOI single-cell CRISPRi screen in K562 cells targeting thousands of candidate enhancers to map enhancer-gene regulation.
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Gene Expression Omnibus ncbi.nlm.nih.gov
Public functional genomics database.
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NCBI E-utilities ncbi.nlm.nih.gov
Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc).
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MIX-Seq nature.com
Multiplexed single-cell transcriptional profiling of chemical and genetic perturbation responses across pools of cancer cell lines.
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PDX-Atlas muralportal.pdxatlas.org
Portal integrating clinical, genomic, transcriptomic, and drug-response data from patient-derived xenograft models.
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MoNA MassBank of North America mona.fiehnlab.ucdavis.edu
Meta-database of metabolite mass spectra, metadata, and associated compounds.
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MoleculeNet moleculenet.ai
Benchmark datasets for molecular machine learning.
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miRBase mirbase.org
Reference repository for microRNA gene annotations, sequences, and experimentally validated targets.
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MIMIC-IV mimic.mit.edu
Freely accessible critical care database.
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MDAnalysis mdanalysis.org
Python library for analyzing and altering molecular dynamics simulation trajectories.
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MassBank massbank.jp
Open source databases and tools for mass spectrometry reference spectra.
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LIPID MAPS lipidmaps.org
Database of lipids.
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LINCS L1000 lincsproject.org
Gene expression profiles (978 landmark genes) for >20,000 chemical and genetic perturbations across cell lines.
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KEGG REST API kegg.jp
API for accessing KEGG pathways, compounds, genes, and reactions.
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BACE kaggle.com
Binary classification and regression dataset for β-secretase 1 (BACE-1) inhibitor binding affinity.
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JASPAR jaspar.genereg.net
Database of transcription factor binding profiles.
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Kinase Inhibitor Bioactivity Data (KIBA) janeliascicomp.github.io
Integrated bioactivity scores for kinase inhibitors combining Ki, Kd, and IC50 measurements.
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1000 Genomes Project internationalgenome.org
Reference panel of human genetic variation from 2,504 individuals across 26 populations.
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DeepDSC ieeexplore-ieee-org.ezp2.lib.umn.edu
Autoencoder + fully connected NN.
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Therapeutic Target Database idrblab.net
Drug-target, target-disease, and drug-disease datasets.
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ICD10 icd.who.int
International Classification of Diseases, 10th revision.
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Human Cell Atlas humancellatlas.org
Open global atlas of all cells in the human body.
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BioMedLM huggingface.co
2.7B parameter GPT-2-style language model trained exclusively on biomedical literature from PubMed for biomedical question answering and text generation.
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Virchow2 huggingface.co
632M-parameter pathology vision transformer pretrained on 3.1M whole-slide images with mixed-magnification self-supervision.
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Virchow huggingface.co
Million-slide digital pathology foundation model using a vision transformer and self-supervised distillation for tile-level pathology image representation.
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Phikon-v2 huggingface.co
Updated pathology foundation model for general-purpose histology feature extraction and transfer learning.
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Phikon huggingface.co
ViT-based pathology foundation model pretrained with iBOT self-supervision on TCGA whole-slide images.
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BiomedCLIP huggingface.co
CLIP-based vision-language foundation model for biomedical images and text trained on PubMed figure–caption pairs.
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Tahoe-100M huggingface.co
Giga-scale single-cell perturbation atlas with >100 million profiles from 50 cancer cell lines exposed to ~1,100 small molecules.
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TCGA virtual spatial transcriptomics atlas huggingface.co
DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: DeepSpot-M.
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