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This is the development version of saseR; for the stable release version, see saseR.

Scalable Aberrant Splicing and Expression Retrieval

Bioconductor version: Development (3.20)

saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{}.

Author: Alexandre Segers [aut, cre], Jeroen Gilis [ctb], Mattias Van Heetvelde [ctb], Elfride De Baere [ctb], Lieven Clement [ctb]

Maintainer: Alexandre Segers <Alexandre.segers at>

Citation (from within R, enter citation("saseR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Main vignette: saseR analyses HTML R Script
Reference Manual PDF


biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Regression, Sequencing, Software
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports ASpli, S4Vectors, BiocGenerics, GenomicFeatures, MASS, PRROC, SummarizedExperiment, edgeR, pracma, precrec, BiocParallel, DESeq2, DEXSeq, data.table, limma, methods, GenomicRanges, GenomicAlignments, rrcov, MatrixGenerics, stats, IRanges, knitr, dplyr, igraph, parallel
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Source Package saseR_1.1.0.tar.gz
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