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trena

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

Bioconductor version: Release (3.17)

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 "4.3") 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")
A Brief Introduction to TReNA HTML R Script
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
Explore output controls HTML R Script
Tiny Vignette Example HTML R Script
TRENA: computational prediction of gene regulation HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.21.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3
Depends R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)
Imports RSQLite, RMySQL, lassopv, randomForest, 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
Linking To
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9
System Requirements
Enhances
URL https://pricelab.github.io/trena/
Bug Reports https://github.com/PriceLab/trena/issues
See More
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_1.21.0.tar.gz
Windows Binary trena_1.22.1.zip
macOS Binary (x86_64) trena_1.22.1.tgz
macOS Binary (arm64) trena_1.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/trena
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/trena
Bioc Package Browser https://code.bioconductor.org/browse/trena/
Package Short Url https://bioconductor.org/packages/trena/
Package Downloads Report Download Stats