Package: regsplice 1.39.0

Lukas M. Weber

regsplice: L1-regularization based methods for detection of differential splicing

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

Authors:Lukas M. Weber [aut, cre]

regsplice_1.39.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
regsplice/json (API)
NEWS

# Install 'regsplice' in R:

install.packages('regsplice', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lmweber/regsplice/issues

On BioConductor:regsplice-1.39.0(bioc 3.24)regsplice-1.38.0(bioc 3.23)

immunooncology alternativesplicing differentialexpression differentialsplicing sequencing rnaseq microarray exonarray experimentaldesign software

5.77 score 3 stars 33 scripts 377 downloads 24 exports 30 dependencies

Last updated from:be97a76629. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	179
linux-devel-x86_64	NOTE	347
source / vignettes	OK	237
linux-release-x86_64	NOTE	312
macos-release-arm64	NOTE	165
macos-oldrel-arm64	NOTE	197
windows-devel	NOTE	234
windows-release	NOTE	389
windows-oldrel	NOTE	214
wasm-release	OK	119

Exports:assays colData countsData createDesignMatrix df_tests filterLowCounts filterZeros fitFullMultiple fitNullMultiple fitRegMultiple gene_IDs initializeResults LR_stats LRTests p_adj p_vals regsplice RegspliceData RegspliceResults rowData runNormalization runVoom summaryTable weightsData

Dependencies:abind Biobase BiocGenerics codetools DelayedArray edgeR foreach generics GenomicRanges glmnet IRanges iterators lattice limma locfit Matrix MatrixGenerics matrixStats pbapply Rcpp RcppEigen S4Arrays S4Vectors Seqinfo shape SparseArray statmod SummarizedExperiment survival XVector

regsplice workflow

Lukas M. Weber, Mark D. Robinson

Rendered fromregsplice-workflow.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-11-28
Started: 2016-10-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create design matrix.	createDesignMatrix
Filter low-count exons.	filterLowCounts
Filter zero-count exons.	filterZeros
Fit models.	fitFullMultiple fitNullMultiple fitRegMultiple
Initialize RegspliceResults object.	initializeResults
Calculate likelihood ratio tests.	LRTests
Wrapper function to run regsplice.	regsplice
RegspliceData objects.	assays,RegspliceData-method colData,RegspliceData-method countsData countsData,RegspliceData-method RegspliceData RegspliceData-class rowData,RegspliceData-method weightsData weightsData,RegspliceData-method [,RegspliceData,ANY,ANY,ANY-method
RegspliceResults objects.	df_tests df_tests,RegspliceResults-method gene_IDs gene_IDs,RegspliceResults-method LR_stats LR_stats,RegspliceResults-method p_adj p_adj,RegspliceResults-method p_vals p_vals,RegspliceResults-method RegspliceResults RegspliceResults-class
Calculate normalization factors.	runNormalization
Calculate 'voom' transformation and weights.	runVoom
Summary table.	summaryTable