/archs-extension

Chrome Extension for ARCHS

Primary LanguageJavaScript

ARCHS4 Chrome Extension

What is ARCHS4?

ARCHS4 (All RNA-seq and CHIP-Seq Signature Search Space) is a web platform and browser extension which enriches the landing pages of RNA-seq datasets available on the Gene Expression Omnibus (GEO) by embedding interfaces to download, interactively visualize and analyze the pre-aligned and pre-processed sequencing data.

What functions does it add?

The ARCHS4 extension enriches GSE landing pages in two ways:

  1. By adding a link to an updated Series Matrix File, containing the gene counts generated from the matching raw sequencing files available on the SRA database.
  2. By adding an interactive heatmap visualization of the expression top 1000 most variable genes, generated using Clustergrammer.

Where is the extension active?

The ARCHS4 extension is currently active on the landing pages of GEO Series (GSE) containing data from human (Homo sapiens) and mouse (Mus musculus) samples generated by high-throughput RNA-sequencing. The extension can be tested on the landing page of GSE77197.

How were the raw sequencing files processed?

Available FASTQ files were downloaded from the SRA database and aligned against the Ensembl references using Kallisto (GRCh38.cdna.all for human data, GRCm38.cdna.all for mouse data). Sample profiles were built by adding all gene counts from corresponding SRA level gene counts.