is a Data Source.
ARCHS4 is a Ma'ayan Lab resource for uniformly processed public RNA-seq data that provides gene and transcript count matrices, metadata search, and interactive exploration for large collections of human and mouse samples aggregated from GEO and SRA.
biomedical, genomics
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| archs4.portal | ARCHS4 Portal | archs4.org | GraphicalInterface | http | Web portal for metadata search, expre... |
| archs4.human.gene_counts | ARCHS4 Human Gene Counts | human_gene_v2.latest.h5 (57.6 GB) | Product | hdf5 | Latest human gene-level ARCHS4 expres... |
| archs4.mouse.gene_counts | ARCHS4 Mouse Gene Counts | mouse_gene_v2.latest.h5 (45.7 GB) | Product | hdf5 | Latest mouse gene-level ARCHS4 expres... |
| archs4.human.transcript_counts | ARCHS4 Human Transcript Counts | human_transcript_v2.latest.h5 (178.8 GB) | Product | hdf5 | Latest human transcript-level ARCHS4 ... |
| archs4.mouse.transcript_counts | ARCHS4 Mouse Transcript Counts | mouse_transcript_v2.latest.h5 (105.8 GB) | Product | hdf5 | Latest mouse transcript-level ARCHS4 ... |
| archs4.zoo | ARCHS4 Zoo Downloads | zoo | Product | hdf5 | Collection page for ARCHS4 Zoo downlo... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| chea-kg.graph | ChEA-KG Database | ❔ | GraphProduct | neo4j | had primary source | Neo4j knowledge graph integrating tra... |
| chea-kg.libraries | ChEA-KG Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
| chea.libraries | ChEA Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
ARCHS4 is a large-scale expression resource that uniformly processes public RNA-seq experiments and exposes the resulting data through interactive web search, visualization, and bulk download interfaces. The current canonical homepage is archs4.org, while the original Ma’ayan Lab deployment remains available as a legacy site.
The public documentation states that ARCHS4 aggregates human and mouse RNA-seq experiments from GEO and SRA, aligns reads with kallisto in a cloud-based processing pipeline, and uses Ensembl annotations for gene and transcript quantification. The current site also notes an ARCHS4 Zoo section for additional species and links to companion client packages such as ARCHS4py and archs4r.
Created: May 21, 2026 | Last modified: May 21, 2026