Package: saseR
Type: Package
Title: Scalable Aberrant Splicing and Expression Retrieval
Date: 2023-06-01
Version: 1.0.0
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
git_url: https://git.bioconductor.org/packages/saseR
git_branch: RELEASE_3_19
git_last_commit: 83a2bb6
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 01:41:17 UTC; biocbuild
Author: Alexandre Segers [aut, cre],
  Jeroen Gilis [ctb],
  Mattias Van Heetvelde [ctb],
  Elfride De Baere [ctb],
  Lieven Clement [ctb]
Maintainer: Alexandre Segers <Alexandre.segers@ugent.be>
Built: R 4.4.0; ; 2024-05-02 13:27:45 UTC; windows
