This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

trena

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of trena; for the stable release version, see trena.

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Bioconductor version: Development (3.18)

Methods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available.

Author: Seth Ament <seth.ament at systemsbiology.org>, Paul Shannon <pshannon at systemsbioloyg.org>, Matthew Richards <mrichard at systemsbiology.org>

Maintainer: Paul Shannon <paul.thurmond.shannon at gmail.com>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("trena")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.23.2
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3
Depends R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)
Imports RSQLite, RMySQL, lassopv, randomForest, xgboost, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA
Linking To
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9
System Requirements
Enhances
URL https://pricelab.github.io/trena/
Bug Reports https://github.com/PriceLab/trena/issues
See More
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
Windows Binary trena_1.23.2.zip
macOS Binary (x86_64) trena_1.23.2.tgz
macOS Binary (arm64) trena_1.23.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/trena
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/trena
Package Short Url https://bioconductor.org/packages/trena/
Package Downloads Report Download Stats