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OutSplice

Comparison of Splicing Events between Tumor and Normal Samples


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OutSplice")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OutSplice")
Find Splicing Outliers in Tumor Samples with OutSplice HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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)
System Requirements
URL https://github.com/GuoLabUCSD/OutSplice
Bug Reports https://github.com/GuoLabUCSD/OutSplice/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package OutSplice_1.2.0.tar.gz
Windows Binary OutSplice_1.2.0.zip
macOS Binary (x86_64) OutSplice_1.2.0.tgz
macOS Binary (arm64) OutSplice_1.2.0.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/
Package Downloads Report Download Stats