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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 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: Release (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>, Paul Shannon <pshannon at>, Matthew Richards <mrichard at>

Maintainer: Paul Shannon <paul.thurmond.shannon at>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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,, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA
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Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9
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