trena

DOI: 10.18129/B9.bioc.trena  

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

Bioconductor version: Release (3.16)

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 "4.2") 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	1.20.0
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	trena_1.20.0.tar.gz
Windows Binary	trena_1.20.0.zip
macOS Binary (x86_64)	trena_1.20.0.tgz
macOS Binary (arm64)	trena_1.20.0.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