trena

DOI: 10.18129/B9.bioc.trena    

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

Bioconductor version: Release (3.6)

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 <pshannon at systemsbiology.org>

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

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

Details

biocViews	FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version	1.0.3
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, RMySQL, DBI, BSgenome, stringr, 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, limma, plyr, knitr, BiocGenerics, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	trena_1.0.3.tar.gz
Windows Binary	trena_0.99.190.zip
Mac OS X 10.11 (El Capitan)	trena_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/trena
Package Short Url	http://bioconductor.org/packages/trena/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive