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TIN

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

Transcriptome instability analysis


Bioconductor version: Development (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")

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

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

Details

biocViews AlternativeSplicing, DifferentialSplicing, ExonArray, GeneExpression, Genetics, Microarray, Software
Version 1.35.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 2.12.0), data.table, impute, aroma.affymetrix
Imports WGCNA, squash, stringr
System Requirements
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Suggests knitr, aroma.light, affxparser, RUnit, BiocGenerics
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Package Archives

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

Source Package TIN_1.35.0.tar.gz
Windows Binary TIN_1.35.0.zip
macOS Binary (x86_64) TIN_1.35.0.tgz
macOS Binary (arm64) TIN_1.35.0.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