transite
This is the released version of transite; for the devel version, see transite.
RNA-binding protein motif analysis
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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), stringr (>= 1.5.1), 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_1.30.0.tar.gz |
| Windows Binary (x86_64) | transite_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |