Man pages for biofiles
An Interface for GenBank/GenPept Flat Files

accessorsAccess the various fields of a GenBank record.
as.gbLocationCreate a 'gbLocation'.
biofiles_biofiles_ is an R package for interfacing with GenBank or...
dbxref-methodsAccess the 'db_xref's of GenBank features
dot-filterFilter gbFeatures from a FeatureTable
dot-selectSelect annotations from a FeatureTable
embl_recordParser for Embl Records.
endGet or set the end position of genomic features
extract-methodsMethod extensions to extraction operator for gbRecord...
featureTable-methodsTabulate Genbank features
fuzzyHas a feature fuzzy locations?
gbFeature-classClass '"gbFeature"'
gbFeatureTable-classClass '"gbFeatureTable"'
gbHeader-classGenerator object for the '"gbHeader"' reference class
gbk_recordParser for GenBank/GenPept records.
gbLocation-classClass '"gbLocation"'
gbLocus-classGenerator object for the '"gbLocus"' reference class
gbRecordRead a GenBank/GenPept or Embl format file.
gbRecord-classClass '"gbRecord"'
gbRecordList-classClass '"gbRecordList"'
gbReference-classGenerator object for the '"gbReference"' reference class
gbReferenceList-classGenerator object for the '"gbReferenceList"' reference class
geneIDReturn the _gene_ qualifiers from GenBank features.
genomeRecordFromNCBIFetch genomes from NCBI
getContigSeqRetrieve the sequence of a contig
getFeatures-methodsGet the feature table from a GenBank record.
getHeader-methodsExtract the header from a '"gbRecord"' object.
getSequence-methodsGet the sequence from a GenBank record.
has_commandTest if an external executable is available
hasKey-methodsHas a feature a specific key?
hasQualif-methodsHas a feature a specific qualifier?
index-methodsAccess the indices of GenBank features
key-methodsGet/set keys of GenBank features
length-methodsGet the number of gbFeatures.
linebreakFormat paragraphs
location-methodsAccess genomic locations of GenBank features
locusTagReturn the _locus_tag_ qualifiers from GenBank features.
manip-methodsReturn a subset of features or annotations from a GenBank...
noteReturn the _note_ qualifiers from GenBank features.
padPad a string
productReturn the _product_ qualifiers from GenBank features.
proteinIDReturn the _protein_id_ qualifiers from GenBank features.
qualifList-methodsList the names of Genbank qualifiers.
qualif-methodsGet/set qualifiers of GenBank features
qualifTable-methodsTabulate Genbank qualifiers
rangesExtract features as '"GRanges"' objects.
revcomp-methodsReverse-complement features in a GenBank record
saveRecord-methodsSave and load 'gbRecord' objects.
seqinfo-classGenerator object for the '"seqinfo"' reference class
shiftShift the location of features in a GenBank record
spanGet the span of genomic features.
startGet or set the start position of genomic features
strandGet or set the strand information of genomic features
summary-methodsSummarise a GenBank record.
translationReturn the _translation_s from GenBank features.
uniqueQualifsQuickly list all qualifier names.
upstreamFind flanking features.
view-methodsView all features in a 'gbFeatureTable'
write.FeatureTable-methodsWrite GenBank records or features to file in Feature Table...
write.GenBank-methodsWrite GenBank records or features to file in GenBank format
biofiles documentation built on May 2, 2019, 3:31 p.m.