OutSplice

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Comparison of Splicing Events between Tumor and Normal Samples

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-0877-5639 , Sandhya Kalavacherla [aut] ORCID: 0000-0003-0485-9042 , Michael Considine [aut] ORCID: 0000-0002-8666-4857 , Bahman Afsari [aut] ORCID: 0000-0001-8717-7199 , Michael F. Ochs [aut], Joseph Califano [aut] ORCID: 0000-0002-4715-6761 , Daria A. Gaykalova [aut] ORCID: 0000-0001-5037-0147 , Elana Fertig [aut] ORCID: 0000-0003-3204-342X , Theresa Guo [cre, aut] ORCID: 0000-0002-1689-3275

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

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

Joseph Bendik, Sandhya Kalavacherla, Michael Considine, Bahman Afsari, Michael F. Ochs, Joseph Califano, Daria A. Gaykalova, Elana Fertig, Theresa Guo. OutSplice: Comparison of Splicing Events between Tumor and Normal Samples. doi:10.18129/B9.bioc.OutSplice, R package version 1.13.0, https://bioconductor.org/packages/OutSplice.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation
Version	1.13.0
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 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), 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

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	OutSplice_1.13.0.tar.gz
Windows Binary (x86_64)	OutSplice_1.13.0.zip
macOS Binary (big-sur-x86_64)	OutSplice_1.13.0.tgz
macOS Binary (sonoma-arm64)	OutSplice_1.13.0.tgz
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