Miscellaneous
17,439 items in 132 lists
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HEST Xenium virtual spatial transcriptomics huggingface.co
DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: DeepSpot-M.
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Geneformer huggingface.co
Context-aware, attention-based deep learning model pretrained on a large corpus of single-cell transcriptomes.
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H-Optimus-1 huggingface.co
1.1B-parameter pathology foundation model trained on billions of histology images from more than one million slides and 800K+ patients.
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H-Optimus-0 huggingface.co
1.1B-parameter histopathology foundation model trained with self-supervised learning on a large multi-center slide corpus.
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UNI2-h huggingface.co
Billion-parameter histopathology vision foundation model for tile-level feature extraction and downstream computational pathology tasks.
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AI4Chem/ChemLLM-7B-Chat huggingface.co
LLM for chemical & molecular science.
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Human Phenotype Ontology (HPO) hpo.jax.org
Standardized vocabulary of phenotypic abnormalities in human disease, linking genes, variants, and clinical features.
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HMDB (Human Metabolome Database) hmdb.ca
Comprehensive database of small molecule metabolites found in the human body.
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The Genotype-Tissue Expression (GTEx) gtexportal.org
Human gene expression and regulation resource.
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MSigDB (Molecular Signatures Database) gsea-msigdb.org
Curated gene sets derived from pathways and biological processes.
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TRRUST v2 grnpedia.org
Manually curated database of human and mouse transcriptional regulatory interactions between transcription factors and their target genes, expanded with literature-derived evidence.
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DrugBank go.drugbank.com
Database of drugs and targets (University of Alberta).
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gnomAD gnomad.broadinstitute.org
Genome Aggregation Database; genetic variation from large-scale sequencing projects.
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SpatialGlue github.com
Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.
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SaProt github.com
Structure-aware protein language model using structure-aware tokens that encode both sequence and backbone geometry for improved function prediction.
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MOFGCN github.com
GCN + heterogeneous network.
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Drug Mechanism Database (DrugMechDB) github.com
Mechanisms of action from drug to disease.
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TOSICA github.com
Transformer-based framework for one-stop interpretable cell-type annotation supporting cross-dataset and cross-species transfer.
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Uni-Mol2 github.com
Scaled molecular pretraining model using atomic, graph, and 3D geometry features, with models up to 1.1B parameters pretrained on 800M conformations.
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Enformer github.com
Transformer model predicting gene expression from DNA sequence.
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HiDRA github.com
Hierarchical network model incorporating gene and pathway-level information for cancer drug response prediction.
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KEGG PATHWAY genome.jp
Collection of pathway maps.
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KEGG DRUG genome.jp
Comprehensive, approved drug information.
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KEGG COMPOUND genome.jp
Collection of small molecules and biopolymers.
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QM9 figshare.com
Quantum chemistry properties for 134K stable small organic molecules computed at DFT level.
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Norman et al. 2019 CRISPRa Perturb-seq figshare.com
Large-scale CRISPR activation Perturb-seq in K562 cells spanning single-gene and combinatorial perturbations.
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FANTOM5 fantom.gsc.riken.jp
Functional annotation of mammalian genome; comprehensive atlas of active enhancers, promoters, and transcription start sites across human and mouse cell types.
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EU Drug Regulating Authorities Clinical Trials DB (EudraCT) eudract.ema.europa.eu
European clinical trial database.
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ENCODE encodeproject.org
Encyclopedia of DNA Elements; regulatory and functional genomic elements across the genome.
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MGnify ebi.ac.uk
Resource for metagenomic and metatranscriptomic data.
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Pfam ebi.ac.uk
Database of protein families described by multiple sequence alignments and hidden Markov models.
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InterPro ebi.ac.uk
Protein families, domains, and functional sites database integrating 14 member databases including Pfam and PROSITE.
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IntAct ebi.ac.uk
Open-source molecular interaction database and analysis system from EMBL-EBI.
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ChEMBL Web Services ebi.ac.uk
REST API for bioactive molecules, targets, and bioassays.
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ChEMBL ebi.ac.uk
Bioactive molecules with drug-like properties.
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ChEBI ebi.ac.uk
Database focused on small chemical compounds.
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DUD-E (Directory of Useful Decoys, Enhanced) dude.docking.org
Structure-based virtual screening benchmark with active ligands and challenging decoy sets across diverse protein targets.
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NCI60 dtp.cancer.gov
Focuses on 60 cancer cell lines and many drugs.
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DrugTargetCommons drugtargetcommons.fimm.fi
Community platform for curating and integrating experimental bioactivity data across drugs and targets.
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DrugCentral drugcentral.org
Online drug compendium with drug mode of action and indication information.
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CLM-X doi.org
Multi-way Transformer foundation model jointly handling RNA-only, ATAC-only, and paired RNA–ATAC single-cell inputs for integration, translation, annotation, and perturbation prediction.
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EXPRESSO doi.org
Supervised treatment-response framework using pretreatment tumor transcriptomics, drug targets, and context-specific biomarkers across multiple cancer types and therapies.
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Atacformer doi.org
Transformer foundation model for scATAC-seq that learns embeddings of cis-regulatory elements for clustering, annotation, and reference mapping.
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MutationProjector doi.org
Pan-cancer genotype foundation model trained on mutations and copy-number alterations from >30K tumors for clinical representation learning.
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SCARF doi.org
Single-cell RNA+ATAC foundation model pretrained on >2.7M cells for multimodal representation, matching, cross-omics translation, and few-shot annotation.
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EpiFoundation doi.org
Foundation model for scATAC-seq using peak-to-gene aligned pretraining for cell representation, annotation, batch correction, and gene-expression prediction.
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HiCFoundation doi.org
Hi-C foundation model pretrained on large-scale chromatin-contact maps for 3D-genome analysis, epigenomic prediction, and single-cell Hi-C adaptation.
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CAPTAIN doi.org
Multimodal foundation model pretrained on co-assayed single-cell RNA and protein for joint representation learning and cross-modal downstream tasks.
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DTLCDR doi.org
Target-based multimodal framework for preclinical cancer drug response prediction and transfer to clinical response, with explicit unseen-drug generalization.
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DisGeNET disgenet.org
Database of gene-disease associations integrating expert-curated and GWAS data.
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