trena

DOI: 10.18129/B9.bioc.trena    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see trena.

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

Bioconductor version: 3.14

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 "4.1") 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")

 

HTML R Script A Brief Introduction to TReNA
HTML Case Study Four: a novel regulator of GATA2 in erythropoieis?
HTML Case Study One: reproduce known regulation of NFE2 by GATA1 in bulk RNA-seq
HTML Case Study Three: reproduce known regulation of NFE2 by GATA1 in bulk RNA-seq
HTML Case Study Two reproduces known regulation of NFE2 by GATA1 in erytrhop RNA-seq
HTML R Script Explore output controls
HTML R Script Tiny Vignette Example
HTML R Script TRENA: computational prediction of gene regulation
PDF   Reference Manual
Text   NEWS

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.16.0
In Bioconductor since BioC 3.6 (R-3.4) (4.5 years)
License GPL-3
Depends R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)
Imports RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost, 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, WGCNA
LinkingTo
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9
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_1.16.0.tar.gz
Windows Binary trena_1.16.0.zip
macOS 10.13 (High Sierra) trena_1.16.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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