# Scalable Aberrant Splicing and Expression Retrieval

## Documentation for package ‘saseR’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

ASpliSE | ASpliSE
BamtoAspliCounts | Converting BAM files to an ASpli-SummarizedExperiment, which contains gene, bin and junction counts.
calculateOffsets | calculating the offsets to perform aberrant expression or splicing analysis.
convertASpli | Converting SummarizedExperiment with different ASpli-counts to gene, bin or junction level counts.
features | features
saseRExample | saseRExample
saseRfindEncodingDim | Determine the optimal number of latent factors to detect outlier gene expression or splicing
saseRfit | Searching for aberrant expression or splicing.
SEbins | SEbins
SEgenes | SEgenes
SEjunctions | SEjunctions