Package: saseR
Type: Package
Title: Scalable Aberrant Splicing and Expression Retrieval
Date: 2023-06-01
Version: 1.6.0
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, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr,
        edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges,
        igraph, IRanges, limma, methods, MASS, MatrixGenerics,
        S4Vectors, stats, SummarizedExperiment, parallel, PRROC
Suggests: rrcov, knitr, txdbmaker
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: 7.3.2
biocViews: DifferentialExpression, DifferentialSplicing, Regression,
        GeneExpression, AlternativeSplicing, RNASeq, Sequencing,
        Software
BugReports: https://github.com/statOmics/saseR/issues
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:27:12 UTC
RemoteUrl: https://github.com/bioc/saseR
RemoteRef: RELEASE_3_22
RemoteSha: 8ee3ecc8652a4a0ad37f1265eb2f7677dd94ce50
NeedsCompilation: no
Packaged: 2025-11-11 17:19:15 UTC; root
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 4.5.2; ; 2025-11-11 17:25:49 UTC; windows
