archs4-database
ARCHS4 Database
Overview
ARCHS4 (All RNA-seq and ChIP-seq Sample and Signature Search) is a resource of uniformly aligned and processed human and mouse RNA-seq data from NCBI GEO and SRA, covering 1 million+ samples. The REST API at https://maayanlab.cloud/archs4/api/ provides gene-level expression profiles, z-score normalized tissue expression, co-expression networks, and sample metadata search — all without authentication. Large-scale bulk queries can also use the downloadable HDF5 expression matrices.
When to Use
- Retrieving tissue-specific or cell-type-specific expression z-scores for a gene of interest across hundreds of tissue types
- Finding genes co-expressed with a query gene (co-expression network construction or guilt-by-association analysis)
- Searching for RNA-seq samples by tissue, disease, or metadata keyword to identify candidate datasets for reanalysis
- Comparing expression profiles of multiple genes across tissues to prioritize candidates for wet-lab follow-up
- Accessing uniformly processed gene expression matrices (HDF5 format) for large-scale cross-study analysis
- Validating differential expression results by checking whether a gene's expression direction matches population-level tissue profiles
- For variant-level population allele frequencies use
gnomad-database; ARCHS4 provides expression evidence only - For Enrichr pathway enrichment from a gene list use
gget-genomic-databases(gget enrichr); ARCHS4 is for expression lookups
Prerequisites
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