DOI: 10.18129/B9.bioc.trena  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trena.

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

Bioconductor version: 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>, Paul Shannon <pshannon at>, Matthew Richards <mrichard at>

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

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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


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,, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA
Suggests RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9
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