transite

DOI: 10.18129/B9.bioc.transite    

RNA-binding protein motif analysis

Bioconductor version: Release (3.8)

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] (<https://orcid.org/0000-0001-8994-3416>), Anna Gattinger [aut] (<https://orcid.org/0000-0001-7094-9279>), Michael Yaffe [ths, cph] (<https://orcid.org/0000-0002-9547-3251>), Ian Cannell [ths] (<https://orcid.org/0000-0001-5832-9210>)

Maintainer: Konstantin Krismer <krismer at mit.edu>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("transite", version = "3.8")

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 1.0.1
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), gridExtra (>= 2.3), methods, parallel, Rcpp (>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils
LinkingTo Rcpp (>= 0.12.18)
Suggests knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0)
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_1.0.1.tar.gz
Windows Binary transite_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) transite_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/transite
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/transite
Package Short Url http://bioconductor.org/packages/transite/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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