saseR
Scalable Aberrant Splicing and Expression Retrieval
Bioconductor version: Release (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Regression, Sequencing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 |
See More
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | saseR_1.2.0.tar.gz |
| Windows Binary (x86_64) | saseR_1.2.0.zip |
| macOS Binary (x86_64) | saseR_1.2.0.tgz |
| macOS Binary (arm64) | saseR_1.1.0.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/ |
| Package Downloads Report | Download Stats |