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clean build & check

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paul-shannon committed Apr 3, 2018
1 parent 62f760b commit 27df2fdd2852c432d691f3ab5ad41a51e0084aa0
@@ -1 +1,3 @@
^.*\.tsv$
build.makefile
@@ -1,8 +1,8 @@
Package: trena
Type: Package
Title: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Version: 1.1.7
Date: 2018-03-03
Version: 1.1.9
Date: 2018-04-03
Author: Seth Ament <seth.ament@systemsbiology.org>, Paul Shannon <pshannon@systemsbioloyg.org>, Matthew Richards <mrichard@systemsbiology.org>
Maintainer: Matthew Richards <mrichard@systemsbiology.org>
Imports:
@@ -17,7 +17,6 @@ Imports:
RMySQL,
DBI,
BSgenome,
stringr,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
157 NAMESPACE
@@ -1,94 +1,65 @@
exportClasses(
Trena,
VarianceFilter,
MotifMatcher,
FootprintFilter,
HumanDHSFilter,
GeneOntologyFilter,
RandomForestSolver
)
# Generated by roxygen2: do not edit by hand
export(
Trena,
Solver,
BayesSpikeSolver,
EnsembleSolver,
LassoPVSolver,
LassoSolver,
PearsonSolver,
RandomForestSolver,
RidgeSolver,
SpearmanSolver,
SqrtLassoSolver,
CandidateFilter,
MotifMatcher,
FootprintFilter,
HumanDHSFilter,
VarianceFilter,
GeneOntologyFilter,
FootprintFinder,
run,
show,
parseChromLocString,
parseDatabaseUri,
getAvailableSolvers
)
exportMethods(
closeDatabaseConnections,
getCandidates,
getAssayData,
getTarget,
getRegulators,
getChromLoc,
getFootprintsForGene,
getFootprintsInRegion,
getGenePromoterRegion,
getGtfGeneBioTypes,
getGtfMoleculeTypes,
getPromoterRegionsAllGenes,
rescalePredictorWeights,
getSequence,
getEncodeRegulatoryTableNames,
getRegulatoryRegions,
getPfms,
findMatchesByChromosomalRegion,
getProximalPromoter,
getRegulatoryChromosomalRegions,
getRegulatoryTableColumnNames,
getGeneModelTableColumnNames,
createGeneModel,
getSolverNames,
assessSnp
)
import(
DBI,
BiocParallel,
glmnet,
methods,
randomForest,
vbsr,
GenomicRanges,
BSgenome,
flare,
lassopv,
MotifDb
)
importFrom(RSQLite, SQLite)
importFrom(RPostgreSQL, PostgreSQL)
importFrom(RMySQL, MySQL)
importFrom(utils, head)
importFrom(stringr, str_match)
importFrom(org.Hs.eg.db, org.Hs.eg.db)
importFrom(BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38)
importFrom(BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19)
importFrom(SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38)
importFrom(Biostrings, IUPAC_CODE_MAP)
importFrom(Biostrings, maxScore)
importFrom(Biostrings, matchPWM)
importFrom(Biostrings, reverseComplement)
importFrom(biomaRt, useMart)
importFrom(biomaRt, getBM)
importFrom(AnnotationDbi, select)
export(BayesSpikeSolver)
export(CandidateFilter)
export(EnsembleSolver)
export(FootprintFilter)
export(FootprintFinder)
export(GeneOntologyFilter)
export(HumanDHSFilter)
export(LassoPVSolver)
export(LassoSolver)
export(MotifMatcher)
export(PearsonSolver)
export(RandomForestSolver)
export(RidgeSolver)
export(Solver)
export(SpearmanSolver)
export(SqrtLassoSolver)
export(Trena)
export(VarianceFilter)
export(getAvailableSolvers)
export(getCandidates)
export(parseChromLocString)
export(parseDatabaseUri)
export(run)
exportMethods(assessSnp)
exportMethods(closeDatabaseConnections)
exportMethods(createGeneModel)
exportMethods(findMatchesByChromosomalRegion)
exportMethods(getAssayData)
exportMethods(getCandidates)
exportMethods(getChromLoc)
exportMethods(getEncodeRegulatoryTableNames)
exportMethods(getFootprintsForGene)
exportMethods(getFootprintsInRegion)
exportMethods(getGeneModelTableColumnNames)
exportMethods(getGenePromoterRegion)
exportMethods(getGtfGeneBioTypes)
exportMethods(getGtfMoleculeTypes)
exportMethods(getPfms)
exportMethods(getPromoterRegionsAllGenes)
exportMethods(getProximalPromoter)
exportMethods(getRegulators)
exportMethods(getRegulatoryChromosomalRegions)
exportMethods(getRegulatoryRegions)
exportMethods(getRegulatoryTableColumnNames)
exportMethods(getSequence)
exportMethods(getSolverNames)
exportMethods(getTarget)
exportMethods(rescalePredictorWeights)
exportMethods(show)
import(BSgenome)
import(BiocParallel)
import(GenomicRanges)
import(MotifDb)
import(RMySQL)
import(RPostgreSQL)
import(flare)
import(glmnet)
import(lassopv)
import(methods)
import(org.Hs.eg.db)
import(randomForest)
import(utils)
import(vbsr)
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