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import(methods)
importFrom(utils, download.file, packageDescription, read.table, browseURL,
as.person, capture.output, str)
importFrom(stats, setNames)
importFrom(tools, file_ext, file_path_sans_ext)
importFrom(httr, GET, content)
importFrom(rjson, fromJSON)
importMethodsFrom(DBI, dbConnect, dbDisconnect,
dbExecute, dbGetQuery,
dbReadTable, dbWriteTable)
importFrom(RSQLite, SQLite)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(UCSC.utils)
import(GenomeInfoDb)
import(AnnotationDbi)
import(GenomicRanges)
import(GenomicFeatures)
importFrom(Biobase, createPackage)
importClassesFrom(BiocIO, BiocFile, CompressedFile)
importFrom(BiocIO, import, FileForFormat)
## rtracklayer only used in R/makeFeatureDbFromUCSC.R
importFrom(rtracklayer, browserSession, trackNames, ucscTables,
ucscTableQuery, getTable, ucscSchema)
importFrom(biomaRt, getBM, listAttributes, listDatasets, listFilters,
listMarts, useDataset, useEnsembl, useEnsemblGenomes)
export(
## makeTxDb.R:
makeTxDb,
## makeTxDbFromUCSC.R:
supportedUCSCtables,
browseUCSCtrack,
makeTxDbFromUCSC,
## makeTxDbFromBiomart.R:
getChromInfoFromBiomart,
makeTxDbFromBiomart,
## makeTxDbFromEnsembl.R:
makeTxDbFromEnsembl,
## makeTxDbFromGRanges.R:
makeTxDbFromGRanges,
## makeTxDbFromGFF.R:
makeTxDbFromGFF,
## makeFeatureDbFromUCSC.R:
supportedUCSCFeatureDbTracks,
supportedUCSCFeatureDbTables,
UCSCFeatureDbTableSchema,
makeFeatureDbFromUCSC,
## makeTxDbPackage.R:
makePackageName,
makeTxDbPackage,
makeTxDbPackageFromUCSC,
makeTxDbPackageFromBiomart,
makeFDbPackageFromUCSC,
supportedMiRBaseBuildValues
)
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