trena

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see trena.

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

DOI: 10.18129/B9.bioc.trena

Bioconductor version: 3.8

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 "3.5") and enter:


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

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("trena")

A Brief Introduction to TReNA HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription

Version 1.4.2

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

License GPL-3

Depends R (>= 3.4.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)

Imports RSQLite, lassopv, randomForest, flare, vbsr, BiocParallel, RPostgreSQL, RMariaDB, 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

System Requirements

URL

Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

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Build Report Build Report

Package Archives

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

Source Package trena_1.4.2.tar.gz

Windows Binary trena_1.4.0.zip

Mac OS X 10.11 (El Capitan) trena_1.4.2.tgz

Source Repository git clone https://git.bioconductor.org/packages/trena

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/trena

Bioc Package Browser https://code.bioconductor.org/browse/trena/

Package Short Url https://bioconductor.org/packages/trena/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.8 Source Archive