recount3: summaries and queries for large-scale RNA-seq expression and splicing

Abstract

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new analysis pipeline. To facilitate access to the data, we provide the and R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

“…The Ensembl pipeline takes into account evidence of functional potential, including transcript expression levels (Intropolis 25 and recount3; ref. 26 ) and evolutionary constraint of the coding region (Phylogenetic Codon Substitution Frequencies, PhyloCSF 27 ). Other factors are CDS length and concordance with the APPRIS 28 principal isoform and the UniProt/Swiss-Prot 29 canonical isoform.…”

OmicsView: Omics data analysis through interactive visual analytics

“…We conducted a comprehensive comparison of OmicsView and 11 other tools for analyzing omics data, including ARCHS4 [14] , Bgee [15] , BIOMEX [16] , DEE2 [17] , Gemma [17] , GEPIA [18] , GXD [19] , OASIS [2] , PaintOmics 3 [20] , PulmonDB [21] , and recount3 [22] . Specifically, the functionality, software usage, data source, disease focus, and analytical output of these software tools have been summarized in Supplementary Table 1 available at https://bit.ly/3HY9ox5 , thereby assisting users in selecting appropriate tools in their research and distinguishing OmicsView.…”

Ten simple rules for large-scale data processing

“…There are many data resources providing preprocessed data that may meet all or nearly all of one’s needs. For example, Recount3 [ 4 , 5 ], ARCHS4 [ 6 ], and refine.bio [ 7 ] provide processed transcriptomic data in various forms and processed with various tool kits. CBioPortal [ 1 , 8 ] provides mutation calls for many cancer studies.…”