OutSplice

DOI: 10.18129/B9.bioc.OutSplice  

Comparison of Splicing Events between Tumor and Normal Samples

Bioconductor version: Release (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>

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")

 

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

Details

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)
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/GuoLabUCSD/OutSplice
BugReports	https://github.com/GuoLabUCSD/OutSplice/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive