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'))

Peer review:

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

On BioConductor:regsplice-1.33.0(bioc 3.21)regsplice-1.32.0(bioc 3.20)

immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware

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

Last updated 2 months agofrom:27b614a610. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macOKDec 19 2024

Exports:assayscolDatacountsDatacreateDesignMatrixdf_testsfilterLowCountsfilterZerosfitFullMultiplefitNullMultiplefitRegMultiplegene_IDsinitializeResultsLR_statsLRTestsp_adjp_valsregspliceRegspliceDataRegspliceResultsrowDatarunNormalizationrunVoomsummaryTableweightsData

Dependencies:abindaskpassBiobaseBiocGenericscodetoolscrayoncurlDelayedArrayedgeRforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglmnethttrIRangesiteratorsjsonlitelatticelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpbapplyR6RcppRcppEigenS4ArraysS4VectorsshapeSparseArraystatmodSummarizedExperimentsurvivalsysUCSC.utilsXVectorzlibbioc

regsplice workflow

Lukas M. Weber, Mark D. Robinson

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

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

Readme and manuals

Help Manual

Help pageTopics
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