bioc-issue-bot
commented
9 months ago Hi @alexandresegers
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: saseR
Type: Package
Title: Scalable Aberrant Splicing and Expression Retrieval
Date: 2023-06-01
Version: 0.99.0
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 (>= 4.1)
Imports: ASpli,
S4Vectors,
BiocGenerics,
GenomicFeatures,
MASS,
PRROC,
SummarizedExperiment,
edgeR,
pracma,
precrec,
BiocParallel,
DESeq2,
DEXSeq,
data.table,
limma,
havok,
methods,
GenomicRanges,
GenomicAlignments,
rrcov,
MatrixGenerics,
stats,
IRanges,
knitr,
dplyr
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:
Regression,
GeneExpression,
AlternativeSplicing,
RNASeq,
Sequencing,
Software
lshep
alexandresegers
DarioS
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