Package: trena
Type: Package
Title: Fit transcriptional regulatory networks using gene expression,
        priors, machine learning
Version: 1.6.1
Date: 2019-06-05
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, 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
Depends: R (>= 3.4.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17)
Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown
VignetteBuilder: knitr
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' 'BayesSpikeSolver.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'
        'SqrtLassoSolver.R' 'Trena.R' 'VarianceFilter.R' 'help.R'
        'sharedFunctions.R' 'utils.R'
Encoding: UTF-8
RoxygenNote: 6.1.1
git_url: https://git.bioconductor.org/packages/trena
git_branch: RELEASE_3_9
git_last_commit: dd13773
git_last_commit_date: 2019-06-05
Date/Publication: 2019-06-05
NeedsCompilation: no
Packaged: 2019-06-06 04:30:33 UTC; biocbuild
Built: R 3.6.0; ; 2019-06-06 14:18:07 UTC; windows
