Package: regsplice 1.33.0

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]

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regsplice.pdf |regsplice.html✨
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-1.33.0(bioc 3.21)regsplice-1.32.0(bioc 3.20)

immunooncology alternativesplicing differentialexpression differentialsplicing sequencing rnaseq microarray exonarray experimentaldesign software

5.86 score 3 stars 27 scripts 171 downloads 24 exports 42 dependencies

Last updated 23 days agofrom:27b614a610. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	NOTE	Nov 19 2024
R-4.5-linux	NOTE	Nov 19 2024
R-4.4-win	NOTE	Nov 19 2024
R-4.4-mac	NOTE	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

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 askpass Biobase BiocGenerics codetools crayon curl DelayedArray edgeR foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges glmnet httr IRanges iterators jsonlite lattice limma locfit Matrix MatrixGenerics matrixStats mime openssl pbapply R6 Rcpp RcppEigen S4Arrays S4Vectors shape SparseArray statmod SummarizedExperiment survival sys UCSC.utils XVector zlibbioc

regsplice workflow

Lukas M. Weber, Mark D. Robinson

Rendered fromregsplice-workflow.Rmdusingknitr::rmarkdownon Nov 19 2024.

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