Package: OutSplice 1.7.1

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_1.7.1.tar.gz
OutSplice_1.7.1.zip(r-4.5)OutSplice_1.7.1.zip(r-4.4)OutSplice_1.7.1.zip(r-4.3)
OutSplice_1.7.1.tgz(r-4.5-any)OutSplice_1.7.1.tgz(r-4.4-any)OutSplice_1.7.0.tgz(r-4.3-any)
OutSplice_1.7.1.tar.gz(r-4.5-noble)OutSplice_1.7.1.tar.gz(r-4.4-noble)
OutSplice_1.7.1.tgz(r-4.4-emscripten)OutSplice_1.7.1.tgz(r-4.3-emscripten)
OutSplice.pdf |OutSplice.html✨
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-1.7.0(bioc 3.21)OutSplice-1.6.0(bioc 3.20)

alternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressionrnaseqsoftwarevariantannotation

4.30 score 1 stars 4 scripts 140 downloads 3 exports 71 dependencies

Last updated 18 days agofrom:683cfbe121. Checks:1 OK, 6 NOTE, 1 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 05 2025
R-4.5-winNOTEFeb 05 2025
R-4.5-macNOTEFeb 05 2025
R-4.5-linuxNOTEFeb 05 2025
R-4.4-winNOTEFeb 05 2025
R-4.4-macNOTEFeb 05 2025
R-4.3-winNOTEFeb 05 2025
R-4.3-macOUTDATEDJan 28 2025

Exports:outspliceAnalysisoutspliceTCGAplotJunctionData

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsvctrsXMLXVectoryaml

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 Feb 05 2025.

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