Led by Software Engineer Rone Charles and Ph.D. candidate Chris Wilks, we submitted an R/Bioconductor package called snapcount, which was accepted and is included in Bioconductor 3.11. snapcount makes it easy to query the powerful Snaptron server using a natural, accessible set of query functions. Specifically, you can query measurements for genes, exons, splice junctions and coverage vectors from the RNA-seq samples indexed in Snaptron. Samples are organized into compilations (e.g. GTEx, TCGA, or SRA) that altogether contain the same studies and summaries in the recount resource. Queries can be filtered to narrow the focus to particular genes or genomic intervals, to events with certain prevalence, to events that do or don’t appear in gene annotation, or to samples with particular metadata.
snapcount complements the recount package, which also allows for searching by coordinates or by HUGO gene names. In general, recount works best when you are interested in all the genes, exons, or splice junctions in a study, whereas snapcount is best for queries over a particular subset of genes or intervals across all or most of the samples in recount2/Snaptron. The more specific your query, the faster and easier it will be to use snapcount.
Please see the vignette, reference manual and other materials linked from the package page for details on how to obtain and use the package.
This is the group’s first Bioconductor package. We thank Kasper Hansen and others in the Bioconductor community for putting us on the right track. Congrats to Rone and Chris on their great work!