OutSplice

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see OutSplice.

Comparison of Splicing Events between Tumor and Normal Samples

Bioconductor version: 3.21

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

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation

Version 1.8.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 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

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Package Archives

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

Source Package OutSplice_1.8.0.tar.gz

Windows Binary (x86_64) OutSplice_1.8.0.zip

macOS Binary (x86_64) OutSplice_1.8.0.tgz

macOS Binary (arm64) OutSplice_1.8.0.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/

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