trena

This package is for version 3.6 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


Bioconductor version: 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>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF
NEWS Text

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.0.3
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, 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
System Requirements
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Suggests RUnit, limma, plyr, knitr, BiocGenerics, rmarkdown
Linking To
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Depends On Me
Imports Me
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Links To Me
Build Report 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
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
Old Source Packages for BioC 3.6 Source Archive