recount3

recount3 provides access to uniformly processed RNA-seq data from human and mouse, enabling download of RangedSummarizedExperiment objects at gene, exon, or exon-exon junction levels along with sample metadata, QC statistics, and sample coverage BigWig files.

Key Features:

• Large-scale data access: Provides access to over 750,000 publicly available human and mouse RNA-seq samples uniformly processed by the Monorail analysis pipeline.
• Multi-level data download: Enables download of RangedSummarizedExperiment objects at gene, exon, or exon-exon junctions level with sample metadata and QC statistics.
• Coverage file access: Provides access to sample coverage BigWig files.
• Flexible data querying: Supports downloading data as study-level summaries or querying for specific exon-exon junctions, genes, samples, or other features.
• Local data processing compatibility: Monorail can process local and/or private data, allowing direct comparison to any study in recount3.

Scientific Applications:

• Public RNA-seq data reuse: Helps biologists maximize the utility of publicly available RNA-seq data.
• Contextualization of new data: Enables improved understanding of newly collected RNA-seq data through comparison to existing large-scale datasets.
• Expression analysis: Supports gene-level expression studies using uniformly processed data from human and mouse samples.
• Splicing analysis: Facilitates exon-exon junction-level investigations of alternative splicing across large sample collections.

Methodology:

Data are uniformly processed by the Monorail analysis pipeline.