trena

DOI: 10.18129/B9.bioc.trena    

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

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("trena")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("trena")

 

HTML R Script A Brief Introduction to TReNA
PDF   Reference Manual
Text   NEWS

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.2.0
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, 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
LinkingTo
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, RMySQL
SystemRequirements
Enhances
URL
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 trena_1.2.0.tar.gz
Windows Binary trena_1.2.0.zip
Mac OS X 10.11 (El Capitan) trena_1.2.0.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 http://bioconductor.org/packages/trena/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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