recount3

recount3 provides uniformly processed RNA-seq data and derived summaries for human and mouse to support comparative and integrative transcriptomic analyses.

Key Features:

• Uniform processing (Monorail): Uses the Monorail analysis pipeline to process over 750,000 publicly available human and mouse RNA-seq samples uniformly.
• Data objects: Supplies RangedSummarizedExperiment objects at the gene, exon, and exon-exon junction levels with associated sample metadata and QC statistics.
• Coverage BigWig files: Provides per-sample coverage BigWig files for nucleotide-level inspection of RNA-seq signal.
• Study coverage: Aggregates 8,679 human studies and 10,088 mouse studies.
• R/Bioconductor packages: Offers the recount3 and snapcount packages to download study-level summaries or query genes, exons, and exon-exon junctions.
• Local processing: The Monorail pipeline can be run on local or private datasets to produce processing consistent with the recount3 repository.

Scientific Applications:

• Comparative analysis: Compare newly generated RNA-seq data against a large, uniformly processed repository for validation and interpretation.
• Data integration and meta-analysis: Integrate uniformly processed datasets across studies to support large-scale genomic and transcriptomic analyses.
• QC-informed interpretation: Use accompanying sample metadata and QC statistics to assess data quality and refine biological inferences.

Methodology:

RNA-seq data are uniformly processed using the Monorail analysis pipeline and exported as RangedSummarizedExperiment objects, per-sample BigWig coverage files, and QC statistics.