/usr/lib/R/site-library/GenomicFeatures/NAMESPACE is in r-bioc-genomicfeatures 1.22.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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importFrom(utils, download.file, installed.packages, read.table, as.person)
importFrom(tools, file_ext, file_path_sans_ext)
importFrom(RCurl, getURL)
importMethodsFrom(DBI, dbCommit, dbConnect,
dbDisconnect, dbExistsTable, dbGetQuery,
dbReadTable, dbWriteTable, dbListTables, dbListFields)
importFrom(RSQLite, SQLite, SQLITE_RO)
importMethodsFrom(RSQLite, dbBegin, dbGetPreparedQuery)
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, useMart)
importFrom(rtracklayer, FileForFormat, import, asBED, asGFF, browserSession,
ucscTableQuery, tableNames, getTable, trackNames, ucscSchema)
importFrom(AnnotationDbi, columns, keys, keytypes, select, mapIds, metadata, dbconn, dbfile, loadDb, saveDb)
exportClasses(TxDb, FeatureDb)
export(
## utils.R:
DEFAULT_CIRC_SEQS,
## makeTxDb.R:
makeTxDb,
## makeTxDbFromUCSC.R:
supportedUCSCtables,
getChromInfoFromUCSC,
makeTxDbFromUCSC,
## makeTxDbFromBiomart.R:
getChromInfoFromBiomart,
makeTxDbFromBiomart,
## 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,
## disjointExons.R:
disjointExons,
## features.R:
features,
## microRNAs.R:
microRNAs,
tRNAs,
## extractTranscriptSeqs.R:
extractTranscriptSeqs,
## extractUpstreamSeqs.R:
extractUpstreamSeqs,
## getPromoterSeq-methods.R:
getPromoterSeq,
## makeTxDbPackage.R:
makeTxDbPackage,
makeTxDbPackageFromUCSC,
makeTxDbPackageFromBiomart,
makeFDbPackageFromUCSC,
supportedMiRBaseBuildValues,
mapToTranscripts, pmapToTranscripts,
mapFromTranscripts, pmapFromTranscripts,
## transcriptLocs2refLocs.R:
transcriptLocs2refLocs,
transcriptWidths,
## coordinate-mapping-methods.R:
mapToTranscripts, pmapToTranscripts,
mapFromTranscripts, pmapFromTranscripts,
## coverageByTranscript.R:
coverageByTranscript,
pcoverageByTranscript,
## Defunct:
makeTranscriptDb,
makeTranscriptDbFromUCSC,
makeTranscriptDbFromBiomart,
makeTranscriptDbFromGFF
)
exportMethods(
species, 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
)
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