Introduction | Functionality | Minimum required packages | Installation from Bioconductor | Inputs | outspliceAnalysis/outspliceTCGA | Phenotype matrix | plotJunctionData | Methodology | Junction RPM normalization | OGSA initial filtering | OGSA outlier analysis | Genomic references | Junction expression normalization | Filter by expression via offsets | Splice Burden Calculation | Junction Plotting | Outputs | outSpliceAnalysis/outSpliceTCGA | References | Session Info
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
OutSplice/json (API)
| # 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
Last updated from:60d4ae860a. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 271 | ||
| linux-devel-x86_64 | NOTE | 508 | ||
| source / vignettes | OK | 428 | ||
| linux-release-x86_64 | NOTE | 482 | ||
| macos-release-arm64 | NOTE | 282 | ||
| macos-oldrel-arm64 | NOTE | 232 | ||
| windows-devel | NOTE | 368 | ||
| windows-release | NOTE | 391 | ||
| windows-oldrel | NOTE | 390 | ||
| wasm-release | OK | 244 |
Exports:outspliceAnalysisoutspliceTCGAplotJunctionData
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenevctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| OutSplice package overview | OutSplice |
| Alternative Splicing Analyses | outspliceAnalysis |
| Alternative Splicing Analysis for TCGA Data | outspliceTCGA |
| Create Plots of Junction Expression | plotJunctionData |
