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transite

RNA-binding protein motif analysis


Bioconductor version: Release (3.18)

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>

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

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

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, Microarray, Software, Transcription, mRNAMicroarray
Version 1.20.1
In Bioconductor since BioC 3.8 (R-3.5) (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), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils
System Requirements C++11
URL https://transite.mit.edu
See More
Suggests knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0)
Linking To Rcpp (>= 1.0.4.8)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package transite_1.20.1.tar.gz
Windows Binary transite_1.20.1.zip
macOS Binary (x86_64) transite_1.20.1.tgz
macOS Binary (arm64) transite_1.20.1.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
Old Source Packages for BioC 3.18 Source Archive