DESCRIPTION

Package: saseR
Type: Package
Title: Scalable Aberrant Splicing and Expression Retrieval
Date: 2023-06-01
Version: 0.99.9
Description: 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}.
Authors@R: c(person("Alexandre", "Segers", role = c("aut","cre"),
                     email = "Alexandre.segers@ugent.be"),
	     person("Jeroen","Gilis", role="ctb",
		     email = "Jeroen.Gilis@ugent.be"),
	     person("Mattias","Van Heetvelde", role="ctb",
		     email = "Mattias.Vanheetvelde@ugent.be"),
	     person("Elfride","De Baere", role="ctb",
		     email = "Elfride.Debaere@ugent.be"),
	     person("Lieven","Clement", role="ctb",
		     email = "Lieven.Clement@ugent.be"))
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
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/statOmics/saseR, https://doi.org/10.1101/2023.06.29.547014
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 7.2.3
biocViews:
    DifferentialExpression, 
    DifferentialSplicing,
    Regression,
    GeneExpression,
    AlternativeSplicing,
    RNASeq,
    Sequencing,
    Software
BugReports:
    https://github.com/statOmics/saseR/issues