/usr/lib/R/site-library/ensembldb/help/AnIndex is in r-bioc-ensembldb 2.2.2-1.
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 | activeFilter global-filters
activeFilter,EnsDb-method global-filters
addFilter global-filters
addFilter,EnsDb-method global-filters
cdsBy EnsDb-exonsBy
cdsBy,EnsDb-method EnsDb-exonsBy
columns,EnsDb-method EnsDb-AnnotationDbi
convertFilter,AnnotationFilter,EnsDb-method convertFilter
convertFilter,AnnotationFilterList,EnsDb-method convertFilter
dbconn EnsDb-class
dbconn,EnsDb-method EnsDb-class
Deprecated Deprecated
disjointExons,EnsDb-method EnsDb-exonsBy
dropFilter global-filters
dropFilter,EnsDb-method global-filters
EnsDb EnsDb
EnsDb-class EnsDb-class
ensDbFromAH makeEnsemblDbPackage
ensDbFromGff makeEnsemblDbPackage
ensDbFromGRanges makeEnsemblDbPackage
ensDbFromGtf makeEnsemblDbPackage
ensembldb-deprecated Deprecated
ensemblVersion EnsDb-class
ensemblVersion,EnsDb-method EnsDb-class
EntrezidFilter Deprecated
ExonidFilter Deprecated
ExonrankFilter Deprecated
exons EnsDb-exonsBy
exons,EnsDb-method EnsDb-exonsBy
exonsBy EnsDb-exonsBy
exonsBy,EnsDb-method EnsDb-exonsBy
exonsByOverlaps,EnsDb-method EnsDb-exonsBy
fetchTablesFromEnsembl makeEnsemblDbPackage
filter global-filters
Filter-classes Filter-classes
fiveUTRsByTranscript,EnsDb-method EnsDb-exonsBy
GenebiotypeFilter Deprecated
GeneidFilter Deprecated
genes EnsDb-exonsBy
genes,EnsDb-method EnsDb-exonsBy
getGeneRegionTrackForGviz EnsDb-utils
getGeneRegionTrackForGviz,EnsDb-method EnsDb-utils
getGenomeFaFile EnsDb-sequences
getGenomeFaFile,EnsDb-method EnsDb-sequences
hasProteinData hasProteinData-EnsDb-method
hasProteinData,EnsDb-method hasProteinData-EnsDb-method
keys,EnsDb-method EnsDb-AnnotationDbi
keytypes,EnsDb-method EnsDb-AnnotationDbi
lengthOf EnsDb-lengths
lengthOf,EnsDb-method EnsDb-lengths
lengthOf,GRangesList-method EnsDb-lengths
listColumns EnsDb-class
listColumns,EnsDb-method EnsDb-class
listEnsDbs listEnsDbs
listGenebiotypes EnsDb-class
listGenebiotypes,EnsDb-method EnsDb-class
listProteinColumns ProteinFunctionality
listTables EnsDb-class
listTables,EnsDb-method EnsDb-class
listTxbiotypes EnsDb-class
listTxbiotypes,EnsDb-method EnsDb-class
listUniprotDbs ProteinFunctionality
listUniprotDbs,EnsDb-method ProteinFunctionality
listUniprotMappingTypes ProteinFunctionality
listUniprotMappingTypes,EnsDb-method ProteinFunctionality
makeEnsembldbPackage makeEnsemblDbPackage
makeEnsemblSQLiteFromTables makeEnsemblDbPackage
mapIds,EnsDb-method EnsDb-AnnotationDbi
metadata EnsDb-class
metadata,EnsDb-method EnsDb-class
OnlyCodingTxFilter Filter-classes
OnlyCodingTxFilter-class Filter-classes
organism EnsDb-class
organism,EnsDb-method EnsDb-class
promoters EnsDb-exonsBy
promoters,EnsDb-method EnsDb-exonsBy
ProtDomIdFilter Filter-classes
ProtDomIdFilter-class Filter-classes
proteins ProteinFunctionality
proteins,EnsDb-method ProteinFunctionality
returnFilterColumns EnsDb-class
returnFilterColumns,EnsDb-method EnsDb-class
returnFilterColumns<- EnsDb-class
returnFilterColumns<-,EnsDb-method EnsDb-class
runEnsDbApp runEnsDbApp
select EnsDb-AnnotationDbi
select,EnsDb-method EnsDb-AnnotationDbi
SeqendFilter Deprecated
seqinfo EnsDb-class
seqinfo,EnsDb-method EnsDb-class
seqlevels EnsDb-class
seqlevels,EnsDb-method EnsDb-class
seqlevels,GRangesFilter-method Filter-classes
seqlevelsStyle EnsDb-seqlevels
seqlevelsStyle,EnsDb-method EnsDb-seqlevels
seqlevelsStyle<- EnsDb-seqlevels
seqlevelsStyle<-,EnsDb-method EnsDb-seqlevels
SeqnameFilter Deprecated
seqnames,GRangesFilter-method Filter-classes
SeqstartFilter Deprecated
SeqstrandFilter Deprecated
show EnsDb-class
show,EnsDb-method EnsDb-class
supportedFilters,EnsDb-method Filter-classes
supportedSeqlevelsStyles EnsDb-seqlevels
supportedSeqlevelsStyles,EnsDb-method EnsDb-seqlevels
threeUTRsByTranscript,EnsDb-method EnsDb-exonsBy
toSAF EnsDb-exonsBy
toSAF,GRangesList-method EnsDb-exonsBy
transcripts EnsDb-exonsBy
transcripts,EnsDb-method EnsDb-exonsBy
transcriptsBy EnsDb-exonsBy
transcriptsBy,EnsDb-method EnsDb-exonsBy
transcriptsByOverlaps,EnsDb-method EnsDb-exonsBy
TxbiotypeFilter Deprecated
TxidFilter Deprecated
TxSupportLevelFilter Filter-classes
TxSupportLevelFilter-class Filter-classes
UniprotDbFilter Filter-classes
UniprotDbFilter-class Filter-classes
UniprotMappingTypeFilter Filter-classes
UniprotMappingTypeFilter-class Filter-classes
updateEnsDb EnsDb-class
updateEnsDb,EnsDb-method EnsDb-class
useMySQL useMySQL-EnsDb-method
useMySQL,EnsDb-method useMySQL-EnsDb-method
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