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Bioconductor - saseR (development version)

saseR

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

Scalable Aberrant Splicing and Expression Retrieval

Bioconductor version: Development (3.22)

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{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} 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{https://doi.org/10.1101/2023.06.29.547014}.

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 ugent.be>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("saseR")

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

Documentation

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

browseVignettes("saseR")

Details biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Regression, Sequencing, Software Version 1.5.1 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License Artistic-2.0 Depends R (>= 4.3.0) Imports ASpli, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr, edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges, igraph, IRanges, limma, methods, MASS, MatrixGenerics, S4Vectors, stats, SummarizedExperiment, parallel, PRROC System Requirements URL https://github.com/statOmics/saseR https://doi.org/10.1101/2023.06.29.547014 Bug Reports https://github.com/statOmics/saseR/issues See More Suggests rrcov, knitr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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