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Package: trena
Type: Package
Title: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Version: 1.3.15
Date: 2018-10-31
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,
lassopv,
randomForest,
flare,
vbsr,
BiocParallel,
RPostgreSQL,
RMySQL,
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,
RMariaDB
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'
RoxygenNote: 6.1.0