/usr/lib/R/site-library/GenomicFeatures/NAMESPACE is in r-bioc-genomicfeatures 1.26.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 | import(methods)
importFrom(stats, setNames)
importFrom(utils, download.file, installed.packages, read.table, browseURL,
as.person, capture.output, str)
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(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, useMart)
importFrom(rtracklayer, FileForFormat, import, asBED, asGFF, browserSession,
ucscTableQuery, tableNames, getTable, trackNames,
ucscSchema)
exportClasses(TxDb, FeatureDb)
export(
## utils.R:
DEFAULT_CIRC_SEQS,
## makeTxDb.R:
makeTxDb, makePackageName,
## makeTxDbFromUCSC.R:
supportedUCSCtables,
browseUCSCtrack,
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
)
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,
mapIdsToRanges, mapRangesToIds
)
|