trena

DOI: 10.18129/B9.bioc.trena    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see trena.

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

Bioconductor version: 3.10

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version	1.8.0
In Bioconductor since	BioC 3.6 (R-3.4) (2.5 years)
License	GPL-3
Depends	R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)
Imports	RSQLite, RMySQL, lassopv, randomForest, flare, vbsr, xgboost, 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, BSgenome.Scerevisiae.UCSC.sacCer3
SystemRequirements
Enhances
URL	https://pricelab.github.io/trena/
BugReports	https://github.com/PriceLab/trena/issues
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_1.8.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	trena_1.8.0.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	https://bioconductor.org/packages/trena/
Package Downloads Report	Download Stats