Package: OutSplice 1.13.0

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_1.13.0.tar.gz
OutSplice_1.13.0.zip(r-4.7)OutSplice_1.13.0.zip(r-4.6)OutSplice_1.13.0.zip(r-4.5)
OutSplice_1.13.0.tgz(r-4.6-any)OutSplice_1.13.0.tgz(r-4.5-any)
OutSplice_1.13.0.tar.gz(r-4.7-any)OutSplice_1.13.0.tar.gz(r-4.6-any)
OutSplice_1.13.0.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.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

4.00 score 1 stars 8 scripts 326 downloads 3 exports 70 dependencies

Last updated from:60d4ae860a. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE296
linux-devel-x86_64NOTE498
source / vignettesOK391
linux-release-x86_64NOTE505
macos-release-arm64NOTE325
macos-oldrel-arm64NOTE298
windows-develNOTE378
windows-releaseNOTE399
windows-oldrelNOTE374
wasm-releaseOK222

Exports:outspliceAnalysisoutspliceTCGAplotJunctionData

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.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 30 2026.

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