Splicejam

Launch Splicejam

Splicejam is a shiny-app resource that visualizes mouse hippocampal subregion- and compartment-specific RNA-seq data described in Farris et al. The purpose of this resource is to provide the community with a user-friendly interface to mine the data for isoform-specific differences across hippocampal subregions (CA1, CA2, CA3, DG) and subcellular compartments (Cell Body, Dendrites).

The RNA-seq data is visualized using sashimi plots that plot RNA-seq coverage data alongside splice junction-spanning sequence reads, using compressed intron genomic coordinates.

Splicejam is also available as an R package and is part of a suite of RNA-seq analysis R packages, collectively called “jampack” which is available through GitHub, see https://github.com/jmw86069/jampack

For vignettes on how to use Splicejam on other RNA-seq datasets go to: https://jmw86069.github.io/splicejam/