Package: OutSplice 1.12.0

Theresa Guo

OutSplice: Comparison of Splicing Events between Tumor and Normal Samples

An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

Authors:Joseph Bendik [aut], Sandhya Kalavacherla [aut], Michael Considine [aut], Bahman Afsari [aut], Michael F. Ochs [aut], Joseph Califano [aut], Daria A. Gaykalova [aut], Elana Fertig [aut], Theresa Guo [cre, aut]

OutSplice_1.12.0.tar.gz
OutSplice_1.12.0.zip(r-4.7)OutSplice_1.12.0.zip(r-4.6)OutSplice_1.12.0.zip(r-4.5)
OutSplice_1.12.0.tgz(r-4.6-any)OutSplice_1.12.0.tgz(r-4.5-any)
OutSplice_1.12.0.tar.gz(r-4.7-any)OutSplice_1.12.0.tar.gz(r-4.6-any)
OutSplice_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OutSplice/json (API)
NEWS

# Install 'OutSplice' in R:
install.packages('OutSplice', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guolabucsd/outsplice/issues

On BioConductor:OutSplice-1.13.0(bioc 3.24)OutSplice-1.12.0(bioc 3.23)

alternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressionrnaseqsoftwarevariantannotation

4.04 score 1 stars 11 scripts 326 downloads 3 exports 69 dependencies

Last updated from:d02f3201f3 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE227
linux-devel-x86_64NOTE508
source / vignettesOK400
linux-release-x86_64NOTE505
macos-release-arm64NOTE241
macos-oldrel-arm64NOTE263
windows-develNOTE364
windows-releaseNOTE346
windows-oldrelNOTE361
wasm-releaseOK227

Exports:outspliceAnalysisoutspliceTCGAplotJunctionData

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenevctrsXMLXVectoryaml

OutSplice

Joseph Bendik, Sandhya Kalavacherla, Michael Considine, Bahman Afsari, Michael F. Ochs, Joseph Califano, Daria A. Gaykalova, Elana Fertig, Theresa Guo

Rendered fromOutSplice.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-02-04
Started: 2023-01-05