Package: trena
Type: Package
Title: Fit transcriptional regulatory networks using gene expression,
        priors, machine learning
Version: 1.20.0
Date: 2022-08-03
Author: Seth Ament <seth.ament@systemsbiology.org>, Paul Shannon <pshannon@systemsbioloyg.org>, Matthew Richards <mrichard@systemsbiology.org>
Maintainer: Paul Shannon <paul.thurmond.shannon@gmail.com>
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
Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17)
Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR,
        markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3,
        BSgenome.Athaliana.TAIR.TAIR9
URL: https://pricelab.github.io/trena/
BugReports: https://github.com/PriceLab/trena/issues
VignetteBuilder: knitr, rmarkdown, formatR, markdown
Description: Methods for reconstructing transcriptional regulatory networks, especially in species
    for which genome-wide TF binding site information is available.
License: GPL-3
biocViews: Transcription, GeneRegulation, NetworkInference,
        FeatureExtraction, Regression, SystemsBiology, GeneExpression
Collate: 'Solver.R' 'BicorSolver.R' 'CandidateFilter.R'
        'EnsembleSolver.R' 'FootprintFinder.R' 'FootprintFilter.R'
        'GeneOntologyFilter.R' 'HumanDHSFilter.R' 'LassoPVSolver.R'
        'LassoSolver.R' 'MotifMatcher.R' 'PCAMax.R' 'PearsonSolver.R'
        'RandomForestSolver.R' 'RidgeSolver.R' 'SpearmanSolver.R'
        'Trena.R' 'VarianceFilter.R' 'XGBoostSolver.R' 'help.R'
        'sharedFunctions.R' 'utils.R'
Encoding: UTF-8
RoxygenNote: 7.2.1
git_url: https://git.bioconductor.org/packages/trena
git_branch: RELEASE_3_16
git_last_commit: 0b1d1b9
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-07
NeedsCompilation: no
Packaged: 2022-11-09 22:23:02 UTC; biocbuild
Built: R 4.2.1; ; 2022-11-10 07:18:05 UTC; unix
