transite

DOI: 10.18129/B9.bioc.transite  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see transite.

RNA-binding protein motif analysis

Bioconductor version: 3.17

transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.

Author: Konstantin Krismer [aut, cre, cph] , Anna Gattinger [aut] , Michael Yaffe [ths, cph] , Ian Cannell [ths]

Maintainer: Konstantin Krismer <krismer at mit.edu>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("transite")

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("transite")

 

HTML	R Script	Spectrum Motif Analysis (SPMA)
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, Microarray, Software, Transcription, mRNAMicroarray
Version	1.18.0
In Bioconductor since	BioC 3.8 (R-3.5) (5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5)
Imports	BiocGenerics(>= 0.26.0), Biostrings(>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges(>= 1.32.6), ggplot2 (>= 3.0.0), ggseqlogo (>= 0.1), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils
LinkingTo	Rcpp (>= 1.0.4.8)
Suggests	knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0)
SystemRequirements	C++11
Enhances
URL	https://transite.mit.edu
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	transite_1.18.0.tar.gz
Windows Binary	transite_1.18.0.zip
macOS Binary (x86_64)	transite_1.18.0.tgz
macOS Binary (arm64)	transite_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/transite
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/transite
Bioc Package Browser	https://code.bioconductor.org/browse/transite/
Package Short Url	https://bioconductor.org/packages/transite/
Package Downloads Report	Download Stats