gschofl/biofiles
An Interface for GenBank/GenPept Flat Files

Package index
Search the gschofl/biofiles package
Vignettes
Functions
416
Source code
37
Man pages
60
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gschofl/biofiles: An Interface for GenBank/GenPept Flat Files
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API

API for gschofl/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
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
gbLocation Source code
gbLocation-class Man page
gbLocus-class 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
gbReferenceList-class 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
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
gschofl/biofiles documentation built on Sept. 27, 2020, 12:08 a.m.

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