This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see trena.
Bioconductor version: 3.9
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 (from within R,
enter citation("trena")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("trena")
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:
browseVignettes("trena")
HTML | R Script | A Brief Introduction to TReNA |
Reference Manual | ||
Text | NEWS |
biocViews | FeatureExtraction, GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription |
Version | 1.6.1 |
In Bioconductor since | BioC 3.6 (R-3.4) (2 years) |
License | GPL-3 |
Depends | R (>= 3.4.0), utils, glmnet (>= 2.0.3), MotifDb(>= 1.19.17) |
Imports | RSQLite, RMySQL, 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, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi |
LinkingTo | |
Suggests | RUnit, plyr, knitr, BiocGenerics, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | trena_1.6.1.tar.gz |
Windows Binary | trena_1.6.1.zip |
Mac OS X 10.11 (El Capitan) | trena_1.6.1.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 |
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