saseR

Scalable Aberrant Splicing and Expression Retrieval


Bioconductor version: Release (3.19)

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 "4.4") and enter:


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

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")
Main vignette: saseR analyses HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Regression, Sequencing, Software
Version 1.0.0
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
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
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Package Archives

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

Source Package saseR_1.0.0.tar.gz
Windows Binary saseR_1.0.0.zip
macOS Binary (x86_64) saseR_1.0.0.tgz
macOS Binary (arm64) saseR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/saseR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/saseR
Bioc Package Browser https://code.bioconductor.org/browse/saseR/
Package Short Url https://bioconductor.org/packages/saseR/
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