transite
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see transite.
RNA-binding protein motif analysis
Bioconductor version: 3.9
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("transite")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, Microarray, Software, Transcription, mRNAMicroarray |
| Version | 1.2.1 |
| 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), ggseqlogo (>= 0.1), gridExtra (>= 2.3), methods, parallel, Rcpp (>= 0.12.18), 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) |
| Linking To | Rcpp (>= 0.12.18) |
| 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_1.2.1.tar.gz |
| Windows Binary | transite_1.2.1.zip |
| Mac OS X 10.11 (El Capitan) | transite_1.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/transite |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |