trena
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: 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>
citation("trena")):
Installation
To install this package, start R (version "4.3") 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")| 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 | ||
| NEWS | Text |
Details
| 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, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA |
| System Requirements | |
| URL | https://pricelab.github.io/trena/ |
| Bug Reports | https://github.com/PriceLab/trena/issues |
See More
| Suggests | RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trena_1.24.0.tar.gz |
| Windows Binary | trena_1.24.0.zip |
| macOS Binary (x86_64) | trena_1.24.0.tgz |
| macOS Binary (arm64) | trena_1.24.0.tgz |
| 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 |