Package: OutSplice 1.7.0

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_1.7.0.tar.gz
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OutSplice_1.7.0.tgz(r-4.4-any)OutSplice_1.7.0.tgz(r-4.3-any)
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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'))

Peer review:

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

On BioConductor:OutSplice-1.5.0(bioc 3.20)OutSplice-1.4.0(bioc 3.19)

alternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressionrnaseqsoftwarevariantannotation

4.18 score 1 stars 4 scripts 106 downloads 3 exports 71 dependencies

Last updated 23 days agofrom:db952c8b42. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:outspliceAnalysisoutspliceTCGAplotJunctionData

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsvctrsXMLXVectoryamlzlibbioc

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 Oct 30 2024.

Last update: 2023-04-18
Started: 2023-01-05