trena

DOI: 10.18129/B9.bioc.trena  

This is the development version of trena; for the stable release version, see trena.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("trena")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version	1.23.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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