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import(methods)
importFrom(stats, setNames)
importFrom(utils, download.file, packageDescription, read.table, browseURL,
as.person, capture.output, str)
importFrom(tools, file_ext, file_path_sans_ext)
importFrom(RCurl, getURL)
importMethodsFrom(DBI, dbConnect, dbDisconnect,
dbExecute, dbGetQuery,
dbReadTable, dbWriteTable, dbListTables,
dbListFields)
importFrom(RSQLite, SQLite, SQLITE_RO)
import(AnnotationDbi)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(XVector)
import(GenomicRanges)
importFrom(Biobase, createPackage)
importClassesFrom(Biostrings, DNAString, DNAStringSet, MaskedDNAString)
importFrom(Biostrings, DNAStringSet, reverseComplement, getSeq)
importFrom(biomaRt, getBM, listAttributes, listDatasets, listFilters,
listMarts, useDataset, useEnsembl, useEnsemblGenomes)
importClassesFrom(BiocIO, BiocFile, CompressedFile)
importFrom(BiocIO, FileForFormat)
importFrom(rtracklayer, import, asBED, asGFF, browserSession,
ucscTableQuery, tableNames, getTable, trackNames,
ucscSchema, ucscTables)
exportClasses(TxDb, FeatureDb)
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,
## id2name.R:
id2name,
## transcripts.R:
transcripts, exons, cds, genes,
## transcriptsBy.R:
transcriptsBy,
exonsBy,
cdsBy,
intronsByTranscript,
fiveUTRsByTranscript,
threeUTRsByTranscript,
## transcriptsByOverlaps.R:
transcriptsByOverlaps,
exonsByOverlaps,
cdsByOverlaps,
## transcriptLengths.R:
transcriptLengths,
## exonicParts.R:
tidyTranscripts, tidyExons, tidyIntrons,
exonicParts, intronicParts,
## disjointExons.R:
disjointExons,
## extendExonsIntoIntrons.R:
extendExonsIntoIntrons,
## features.R:
features,
## microRNAs.R:
microRNAs,
tRNAs,
## extractTranscriptSeqs.R:
extractTranscriptSeqs,
## extractUpstreamSeqs.R:
extractUpstreamSeqs,
## getPromoterSeq-methods.R:
getPromoterSeq,
## makeTxDbPackage.R:
makePackageName,
makeTxDbPackage,
makeTxDbPackageFromUCSC,
makeTxDbPackageFromBiomart,
makeFDbPackageFromUCSC,
supportedMiRBaseBuildValues,
mapToTranscripts, pmapToTranscripts,
mapFromTranscripts, pmapFromTranscripts,
## transcriptLocs2refLocs.R:
transcriptLocs2refLocs,
transcriptWidths,
## coordinate-mapping-methods.R:
mapToTranscripts, pmapToTranscripts,
mapFromTranscripts, pmapFromTranscripts,
## proteinToGenome.R:
proteinToGenome,
## coverageByTranscript.R:
coverageByTranscript,
pcoverageByTranscript
)
exportMethods(
organism,
show,
as.list,
seqlevels0, "seqlevels<-", seqinfo,
transcripts, exons, cds, genes,
promoters,
transcriptsByOverlaps,
exonsByOverlaps,
cdsByOverlaps,
transcriptsBy,
exonsBy,
cdsBy,
intronsByTranscript,
fiveUTRsByTranscript,
threeUTRsByTranscript,
disjointExons,
microRNAs,
tRNAs,
extractTranscriptSeqs,
extractUpstreamSeqs,
getPromoterSeq,
isActiveSeq,
"isActiveSeq<-",
asBED, asGFF,
distance,
mapToTranscripts, pmapToTranscripts,
mapFromTranscripts, pmapFromTranscripts,
mapIdsToRanges, mapRangesToIds,
proteinToGenome
)
|
