DOI: 10.18129/B9.bioc.trena    

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

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("trena", version = "3.8")


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biocViews FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription
Version 1.4.0
License GPL-3
Depends R (>= 3.4.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17)
Imports RSQLite, lassopv, randomForest, flare, vbsr, BiocParallel, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38,, Biostrings, GenomicRanges, biomaRt, AnnotationDbi
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, RMariaDB
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