OutSplice

DOI: 10.18129/B9.bioc.OutSplice  

This is the development version of OutSplice; for the stable release version, see OutSplice.

Comparison of Splicing Events between Tumor and Normal Samples

Bioconductor version: Development (3.19)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("OutSplice")

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

Documentation

PDF		Reference Manual

Details

biocViews	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation
Version	1.3.0
In Bioconductor since	BioC 3.17 (R-4.3) (0.5 years)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/OutSplice
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OutSplice
Package Short Url	https://bioconductor.org/packages/OutSplice/
Package Downloads Report	Download Stats