DOI: 10.18129/B9.bioc.OutSplice  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see OutSplice.

Comparison of Splicing Events between Tumor and Normal Samples

Bioconductor version: 3.17

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.

Author: 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]

Maintainer: Theresa Guo <twguo at health.ucsd.edu>

Citation (from within R, enter citation("OutSplice")):


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HTML R Script Find Splicing Outliers in Tumor Samples with OutSplice
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biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation
Version 1.0.1
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License GPL-2
Depends R (>= 4.3)
Imports AnnotationDbi(>= 1.60.0), GenomicRanges(>= 1.49.0), GenomicFeatures(>= 1.50.2), IRanges(>= 2.32.0), org.Hs.eg.db(>= 3.16.0), Repitools(>= 1.44.0), TxDb.Hsapiens.UCSC.hg19.knownGene(>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene(>= 3.16.0), S4Vectors(>= 0.36.0)
Suggests BiocStyle, knitr, rmarkdown, testthat
URL https://github.com/GuoLabUCSD/OutSplice
BugReports https://github.com/GuoLabUCSD/OutSplice/issues
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Source Package OutSplice_1.0.1.tar.gz
Windows Binary OutSplice_1.0.1.zip
macOS Binary (x86_64) OutSplice_1.0.1.tgz
macOS Binary (arm64) OutSplice_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/OutSplice
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OutSplice
Bioc Package Browser https://code.bioconductor.org/browse/OutSplice/
Package Short Url https://bioconductor.org/packages/OutSplice/
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