biofiles
An Interface for GenBank/GenPept Flat Files

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Functions
422
Source code
38
Man pages
60
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biofiles: An Interface for GenBank/GenPept Flat Files
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API

API for biofiles
An Interface for GenBank/GenPept Flat Files

Global functions
$,gbFeature-method Man page
.GRanges Source code
.IRanges Source code
.access Source code
.filter Man page Source code
.gbFeatureTable_replace_end Source code
.gbFeatureTable_replace_start Source code
.gbFeature_replace_end Source code
.gbFeature_replace_start Source code
.gbFeature_replace_strand Source code
.gbHeader Man page
.gbLocation_replace_end Source code
.gbLocation_replace_start Source code
.gbLocation_replace_strand Source code
.gbLocus Man page
.gbReference Man page
.gbReferenceList Man page
.get_table_feature Source code
.onLoad Source code
.qual_access Source code
.return Source code
.revcomp Source code
.select Man page
.seq_access Source code
.shift Source code
.simplify Source code
.writeGenBank Source code
.write_feature_table Source code
Call Source code
Compose Source code
Partial Source code
[,gbFeatureTable,character,missing-method Man page
[,gbFeatureTable,logical,missing-method Man page
[,gbFeatureTable,missing,missing-method Man page
[,gbFeatureTable,numeric,missing-method Man page
[,gbRecord,ANY,missing-method Man page
[,gbRecord,missing,missing-method Man page
[[,gbFeature,character,missing-method Man page
[[,gbFeatureTable,ANY,ANY-method Man page
[[,gbRecord,ANY,ANY-method Man page
all_empty Source code
are_empty Source code
as.gbLocation Man page Source code
biofiles Man page
biofiles-package Man page
chooseFromList Source code
collapse Source code
compact Source code
compactChar Source code
compactNA Source code
compactXX Source code
contentLength Source code
count_re Source code
dbxref Man page
dbxref,gbFeature-method Man page
dbxref,gbFeatureTable-method Man page
dbxref,gbRecord-method Man page
dots Source code
downstream Man page Source code
dup Source code
ellipsize Source code
embl_header Source code
embl_line Source code
embl_locus Source code
embl_record Man page Source code
embl_reference Source code
embl_reference_list Source code
end Man page
end,gbFeature-method Man page
end,gbFeatureTable-method Man page
end,gbLocation-method Man page
end,gbRecord-method Man page
end,gbRecordList-method Man page
end<- Man page
end<-,gbFeature-method Man page
end<-,gbFeatureTable-method Man page
end<-,gbLocation-method Man page
featureTable Man page
featureTable,gbFeatureTable-method Man page
featureTable,gbRecord-method Man page
featureTable,gbRecordList-method Man page
fetchGbRecords Source code
fetchHeader Source code
filter Man page
filter,gbFeatureTable-method Man page
filter,gbRecord-method Man page
filter,gbRecordList-method Man page
find_neighbors Source code
flanking Man page Source code
ft Man page
ft,gbRecord-method Man page
ft,gbRecordList-method Man page
fuzzy Man page
fuzzy,gbFeature-method Man page
fuzzy,gbFeatureTable-method Man page
fuzzy,gbLocation-method Man page
fuzzy,gbRecord-method Man page
fuzzy,gbRecordList-method Man page
gbFeature Source code
gbFeature-class Man page
gbFeatureTable-class Man page
gbHeader-class Man page Man page
gbLocation Source code
gbLocation-class Man page
gbLocus-class Man page Man page
gbReader Source code
gbRecord Man page Source code
gbRecord-class Man page
gbRecordList Man page Source code
gbRecordList-class Man page
gbReference-class Man page Man page
gbReferenceList-class Man page Man page
gbk_header Source code
gbk_locus Source code
gbk_record Man page Source code
gbk_reference Source code
gbk_reference_list Source code
geneID Man page
genomeRecordFromNCBI Man page Source code
getAccession Man page
getAccession,gbFeature-method Man page
getAccession,gbFeatureTable-method Man page
getAccession,gbLocation-method Man page
getAccession,gbRecord-method Man page
getAccession,gbRecordList-method Man page
getAccession,seqinfo-method Man page
getComment Man page
getComment,gbFeature-method Man page
getComment,gbFeatureTable-method Man page
getComment,gbRecord-method Man page
getComment,gbRecordList-method Man page
getComment,seqinfo-method Man page
getContigSeq Man page Source code
getDBLink Man page
getDBLink,gbFeature-method Man page
getDBLink,gbFeatureTable-method Man page
getDBLink,gbRecord-method Man page
getDBLink,gbRecordList-method Man page
getDBLink,seqinfo-method Man page
getDBSource Man page
getDBSource,gbFeature-method Man page
getDBSource,gbFeatureTable-method Man page
getDBSource,gbRecord-method Man page
getDBSource,gbRecordList-method Man page
getDBSource,seqinfo-method Man page
getDate Man page
getDate,gbFeature-method Man page
getDate,gbFeatureTable-method Man page
getDate,gbRecord-method Man page
getDate,gbRecordList-method Man page
getDate,seqinfo-method Man page
getDefinition Man page
getDefinition,gbFeature-method Man page
getDefinition,gbFeatureTable-method Man page
getDefinition,gbRecord-method Man page
getDefinition,gbRecordList-method Man page
getDefinition,seqinfo-method Man page
getDivision Man page
getDivision,gbFeature-method Man page
getDivision,gbFeatureTable-method Man page
getDivision,gbRecord-method Man page
getDivision,gbRecordList-method Man page
getDivision,seqinfo-method Man page
getFeatures Man page
getFeatures,gbRecord-method Man page
getFeatures,gbRecordList-method Man page
getGeneID Man page
getGeneID,gbFeature-method Man page
getGeneID,gbFeatureTable-method Man page
getGeneID,gbRecord-method Man page
getGeneID,gbRecordList-method Man page
getGeneID,seqinfo-method Man page
getHeader Man page
getHeader,gbFeature-method Man page
getHeader,gbFeatureTable-method Man page
getHeader,gbRecord-method Man page
getKeywords Man page
getKeywords,gbFeature-method Man page
getKeywords,gbFeatureTable-method Man page
getKeywords,gbRecord-method Man page
getKeywords,gbRecordList-method Man page
getKeywords,seqinfo-method Man page
getLength Man page
getLength,gbFeature-method Man page
getLength,gbFeatureTable-method Man page
getLength,gbRecord-method Man page
getLength,gbRecordList-method Man page
getLength,seqinfo-method Man page
getLocus Man page
getLocus,gbFeature-method Man page
getLocus,gbFeatureTable-method Man page
getLocus,gbRecord-method Man page
getLocus,gbRecordList-method Man page
getLocus,seqinfo-method Man page
getMoltype Man page
getMoltype,gbFeature-method Man page
getMoltype,gbFeatureTable-method Man page
getMoltype,gbRecord-method Man page
getMoltype,gbRecordList-method Man page
getMoltype,seqinfo-method Man page
getOrganism Man page
getOrganism,gbFeature-method Man page
getOrganism,gbFeatureTable-method Man page
getOrganism,gbRecord-method Man page
getOrganism,gbRecordList-method Man page
getOrganism,seqinfo-method Man page
getReference Man page
getReference,gbFeature-method Man page
getReference,gbFeatureTable-method Man page
getReference,gbRecord-method Man page
getReference,gbRecordList-method Man page
getReference,seqinfo-method Man page
getSequence Man page
getSequence,gbFeature-method Man page
getSequence,gbFeatureTable-method Man page
getSequence,gbRecord-method Man page
getSequence,gbRecordList-method Man page
getSource Man page
getSource,gbFeature-method Man page
getSource,gbFeatureTable-method Man page
getSource,gbRecord-method Man page
getSource,gbRecordList-method Man page
getSource,seqinfo-method Man page
getTaxonomy Man page
getTaxonomy,gbFeature-method Man page
getTaxonomy,gbFeatureTable-method Man page
getTaxonomy,gbRecord-method Man page
getTaxonomy,gbRecordList-method Man page
getTaxonomy,seqinfo-method Man page
getTopology Man page
getTopology,gbFeature-method Man page
getTopology,gbFeatureTable-method Man page
getTopology,gbRecord-method Man page
getTopology,gbRecordList-method Man page
getTopology,seqinfo-method Man page
getVersion Man page
getVersion,gbFeature-method Man page
getVersion,gbFeatureTable-method Man page
getVersion,gbRecord-method Man page
getVersion,gbRecordList-method Man page
getVersion,seqinfo-method Man page
get_compounds Source code
get_loc Source code
hasKey Man page
hasKey,gbFeature-method Man page
hasKey,gbFeatureTable-method Man page
hasKey,gbRecord-method Man page
hasKey,gbRecordList-method Man page
hasQualif Man page
hasQualif,gbFeature-method Man page
hasQualif,gbFeatureTable-method Man page
hasQualif,gbRecord-method Man page
hasQualif,gbRecordList-method Man page
has_command Man page Source code
header Man page
header,gbFeature-method Man page
header,gbFeatureTable-method Man page
header,gbRecord-method Man page
index Man page
index,gbFeature-method Man page
index,gbFeatureTable-method Man page
index,gbRecord-method Man page
index,gbRecordList-method Man page
is.embl Source code
is.empty Source code
is.gbk Source code
is_compound Source code
is_feature Source code
is_in Source code
is_index Source code
is_key Source code
is_range Source code
ixsplit Source code
join_seq Source code
joint_range Man page
joint_range,gbFeature-method Man page
joint_range,gbFeatureTable-method Man page
joint_range,gbLocation-method Man page
key Man page
key,gbFeature-method Man page
key,gbFeatureTable-method Man page
key,gbRecord-method Man page
key,gbRecordList-method Man page
key<- Man page
key<-,gbFeature-method Man page
length,gbRecord-method Man page
linebreak Man page Source code
loadRecord Man page Source code
location Man page
location,gbFeature-method Man page
location,gbFeatureTable-method Man page
location,gbRecord-method Man page
locusTag Man page
make_progress_bar Source code
match_idx Source code
merge_dups Source code
merge_seq Source code
merge_split Source code
modify_list Source code
new_gbRecord Man page
note Man page
pad Man page
parse_dbsource Source code
parse_features Source code
parse_gb_record Source code
parse_keys Source code
parse_range Source code
parse_sequence Source code
product Man page
proteinID Man page
qualif Man page
qualif,gbFeature-method Man page
qualif,gbFeatureTable-method Man page
qualif,gbRecord-method Man page
qualif<- Man page
qualif<-,gbFeature-method Man page
qualifList Man page
qualifList,gbFeature-method Man page
qualifList,gbFeatureTable-method Man page
qualifList,gbRecord-method Man page
qualifTable Man page
qualifTable,gbFeatureTable-method Man page
qualifTable,gbRecord-method Man page
qualifTable,gbRecordList-method Man page
ranges Man page
ranges,gbFeature-method Man page
ranges,gbFeatureTable-method Man page
ranges,gbRecord-method Man page
ranges,gbRecordList-method Man page
re Source code
recycle Source code
replace_ext Source code
revcomp Man page
revcomp,gbFeatureTable-method Man page
revcomp,gbRecord-method Man page
saveRecord Man page
saveRecord,gbRecord-method Man page
saveRecord,gbRecordList-method Man page
select Man page
select,gbFeatureTable-method Man page
select,gbRecord-method Man page
select,gbRecordList-method Man page
seqinfo Man page
seqinfo-class Man page Man page
set_reference Source code
shift Man page
shift,gbFeature-method Man page
shift,gbFeatureTable-method Man page
shift,gbLocation-method Man page
shift,gbRecord-method Man page
show_gbFeature Source code
show_gbRecord Source code
span Man page
span,gbFeature-method Man page
span,gbFeatureTable-method Man page
span,gbLocation-method Man page
span,gbRecord-method Man page
span,gbRecordList-method Man page
start Man page
start,gbFeature-method Man page
start,gbFeatureTable-method Man page
start,gbLocation-method Man page
start,gbRecord-method Man page
start,gbRecordList-method Man page
start<- Man page
start<-,gbFeature-method Man page
start<-,gbFeatureTable-method Man page
start<-,gbLocation-method Man page
strand Man page
strand,gbFeature-method Man page
strand,gbFeatureTable-method Man page
strand,gbLocation-method Man page
strand,gbRecord-method Man page
strand,gbRecordList-method Man page
strand<- Man page
strand<-,gbFeature-method Man page
strand<-,gbFeatureTable-method Man page
strand<-,gbLocation-method Man page
strsplitN Source code
summary Man page
summary,gbFeature-method Man page
summary,gbFeatureTable-method Man page
summary,gbRecord-method Man page
summary,gbRecordList-method Man page
tbl_merge Source code
tbl_qual Source code
translation Man page Source code
trim Source code
uniqueQualifs Man page
update_indices Source code
update_split Source code
upstream Man page Source code
view Man page
view,gbFeatureTable-method Man page
with_c_locale Source code
wrap Source code
write.FeatureTable Man page
write.FeatureTable,gbFeatureTable-method Man page
write.FeatureTable,gbRecord-method Man page
write.GenBank Man page
write.GenBank,gbFeatureTable-method Man page
write.GenBank,gbRecord-method Man page
biofiles documentation built on May 2, 2019, 3:31 p.m.

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