TIN

Transcriptome instability analysis

Bioconductor version: Release (3.19)

The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.

Author: Bjarne Johannessen, Anita Sveen and Rolf I. Skotheim

Maintainer: Bjarne Johannessen <bjajoh at rr-research.no>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("TIN")

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("TIN")

Introduction to the TIN package	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DifferentialSplicing, ExonArray, GeneExpression, Genetics, Microarray, Software
Version	1.36.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 years)
License	Artistic-2.0
Depends	R (>= 2.12.0), data.table, impute, aroma.affymetrix
Imports	WGCNA, squash, stringr
System Requirements
URL

Suggests	knitr, aroma.light, affxparser, RUnit, BiocGenerics
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	TIN_1.36.0.tar.gz
Windows Binary (x86_64)	TIN_1.36.0.zip
macOS Binary (x86_64)	TIN_1.36.0.tgz
macOS Binary (arm64)	TIN_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TIN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TIN
Bioc Package Browser	https://code.bioconductor.org/browse/TIN/
Package Short Url	https://bioconductor.org/packages/TIN/
Package Downloads Report	Download Stats