spliceTerrain is an R package for visualising RNA-seq splice patterns as sashimi plots.
It combines fragment-level coverage, splice junction support, and optional
transcript annotation to inspect local splicing patterns across a genomic region.
spliceTerrain was designed to integrate seamlessly within the Bioconductor ecosystem, keeping the workflow entirely within R to support reproducible, customisable splicing visualisation for exploratory analysis, reporting, and publication-quality figures.
BiocManager is recommended for the installation of spliceTerrain.
The development version can be installed from GitHub.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("baerlachlan/spliceTerrain")
At a minimum, we require BAM file paths and a genomic interval to plot.
Here we use BAM files from the RNAseqData.HNRNPC.bam.chr14 package as example data, selecting two of these files to showcase spliceTerrain.
In the most simple case, a genomic interval can be specified as a character vector of length 1.
That's all we need to build a simple sashimi plot!
library(spliceTerrain)
library(RNAseqData.HNRNPC.bam.chr14)
bams <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[c(7, 1)]
region <- "chr14:70,233,810-70,238,690"
spliceTerrain(bam = bams, region = region)
