Curated Academic & Computational Resources

Largest public repository of functional genomics data, including bulk RNA-seq, microarrays, and single-cell studies.

Major European archive of functional genomics experiments with curated metadata and raw sequencing assays.

Comprehensive multi-omics data for 33 cancer types including RNA-seq, somatic mutations, CNVs, and clinical survival profiles.

Comprehensive tissue-specific gene expression reference data from non-diseased healthy human donors across 54 body sites.

International Cancer Genome Consortium global database for uniform cancer genomic and transcriptomic datasets.

Primary NCBI/NIH global archive for raw high-throughput sequencing data (FASTQ, BAM, and CRAM formats).

NCI unified cancer data repository with standardized bioinformatics pipelines, harmonized clinical data, and BAM files.

European counterpart to SRA maintained by EMBL-EBI, containing raw reads, assembled genomes, and functional annotations.

Interactive web platform for exploring and analyzing over 6,500 harmonized GEO RNA-seq datasets with pre-computed counts.

Interactive explorer and open data portal for large-scale standardized single-cell transcriptomic datasets (CZ CELLxGENE).

Systematic, curated collection of scRNA-seq experiments with standardized quality control and re-analysis by EMBL-EBI.

Global collaborative initiative mapping every cell type in the human body across development, health, and disease.

Broad Institute interactive web portal for browsing, visualizing, and sharing published single-cell and spatial studies.

Marker-focused database for human and mouse single-cell transcriptomics with curated cell-type specific gene sets.

Comprehensive single-cell RNA-seq database dedicated to profiling the tumor microenvironment across various human malignancies.

High-value reference database and multimodal atlas of cell types in the human, non-human primate, and mouse brain.

Benchmark healthy human multi-organ transcriptomic atlas comprising over 500,000 cells across 24 distinct tissues.

National Institute on Aging repository for multi-omic and single-cell datasets focused on Alzheimer's disease and neurodegeneration.

NCBI Gene Expression Omnibus repository containing tens of thousands of raw 10x Genomics, Drop-seq, and Smart-seq2 datasets.

European functional genomics archive hosting single-cell study metadata, processed matrices, and FASTQ accessions.

Open-access general research repository hosting large-scale supplementary matrices, AnnData `.h5ad` files, and Seurat `.rds` objects.

Online open-access repository for researchers to preserve, cite, and share supplementary biological datasets and computational figures.

World's largest open database of chemical molecules, structures, bioassays, and biological activities maintained by NCBI.

Manually curated database of bioactive molecules with drug-like properties, binding affinities, and quantitative SAR data.

Comprehensive structured pharmaceutical knowledgebase combining detailed chemical, pharmacological, and drug-target interaction data.

Free database of over 230 million commercially-available 3D chemical structures prepared for virtual screening and docking.

Public database of experimentally measured binding affinities, focusing on the interactions of target proteins with drug candidates.

Primary international archive for 3D experimental structural data of proteins, nucleic acids, and complex biological assemblies.

Dictionary and ontology of small molecular entities focused on biologically relevant chemical compounds.

Comprehensive, high-quality, and freely accessible resource of protein sequence, functional annotation, and structural mapping.

Integrated data warehouse and knowledge discovery system for target prioritization, network analysis, and validation.

Largest international registry and results database of publicly and privately supported clinical studies conducted worldwide.