A B D E F G H I J K L N P Q R S T U W misc
biofiles-package | _biofiles_ is an R package for interfacing with GenBank or Embl flat file records. |
as.gbLocation | Create a 'gbLocation'. |
biofiles | _biofiles_ is an R package for interfacing with GenBank or Embl flat file records. |
dbxref | Access the 'db_xref's of GenBank features |
dbxref-method | Access the 'db_xref's of GenBank features |
downstream | Find flanking features. |
end | Get or set the end position of genomic features |
end-method | Get or set the end position of genomic features |
end<- | Get or set the end position of genomic features |
end<--method | Get or set the end position of genomic features |
featureTable | Tabulate Genbank features |
featureTable-method | Tabulate Genbank features |
filter | Return a subset of features or annotations from a GenBank Record |
filter-method | Return a subset of features or annotations from a GenBank Record |
flanking | Find flanking features. |
ft | Get the feature table from a GenBank record. |
ft-method | Get the feature table from a GenBank record. |
fuzzy | Has a feature fuzzy locations? |
fuzzy-method | Has a feature fuzzy locations? |
gbFeature-class | Class '"gbFeature"' |
gbFeatureTable-class | Class '"gbFeatureTable"' |
gbRecord | Read a GenBank/GenPept or Embl format file. |
gbRecord-class | Class '"gbRecord"' |
gbRecordList | Class '"gbRecordList"' |
gbRecordList-class | Class '"gbRecordList"' |
geneID | Return the _gene_ qualifiers from GenBank features. |
getAccession | Access the various fields of a GenBank record. |
getAccession-method | Access the various fields of a GenBank record. |
getComment | Access the various fields of a GenBank record. |
getComment-method | Access the various fields of a GenBank record. |
getDate | Access the various fields of a GenBank record. |
getDate-method | Access the various fields of a GenBank record. |
getDBLink | Access the various fields of a GenBank record. |
getDBLink-method | Access the various fields of a GenBank record. |
getDBSource | Access the various fields of a GenBank record. |
getDBSource-method | Access the various fields of a GenBank record. |
getDefinition | Access the various fields of a GenBank record. |
getDefinition-method | Access the various fields of a GenBank record. |
getDivision | Access the various fields of a GenBank record. |
getDivision-method | Access the various fields of a GenBank record. |
getFeatures | Get the feature table from a GenBank record. |
getFeatures-method | Get the feature table from a GenBank record. |
getGeneID | Access the various fields of a GenBank record. |
getGeneID-method | Access the various fields of a GenBank record. |
getHeader | Extract the header from a '"gbRecord"' object. |
getHeader-method | Extract the header from a '"gbRecord"' object. |
getKeywords | Access the various fields of a GenBank record. |
getKeywords-method | Access the various fields of a GenBank record. |
getLength | Access the various fields of a GenBank record. |
getLength-method | Access the various fields of a GenBank record. |
getLocus | Access the various fields of a GenBank record. |
getLocus-method | Access the various fields of a GenBank record. |
getMoltype | Access the various fields of a GenBank record. |
getMoltype-method | Access the various fields of a GenBank record. |
getOrganism | Access the various fields of a GenBank record. |
getOrganism-method | Access the various fields of a GenBank record. |
getReference | Access the various fields of a GenBank record. |
getReference-method | Access the various fields of a GenBank record. |
getSequence | Get the sequence from a GenBank record. |
getSequence-method | Get the sequence from a GenBank record. |
getSource | Access the various fields of a GenBank record. |
getSource-method | Access the various fields of a GenBank record. |
getTaxonomy | Access the various fields of a GenBank record. |
getTaxonomy-method | Access the various fields of a GenBank record. |
getTopology | Access the various fields of a GenBank record. |
getTopology-method | Access the various fields of a GenBank record. |
getVersion | Access the various fields of a GenBank record. |
getVersion-method | Access the various fields of a GenBank record. |
hasKey | Has a feature a specific key? |
hasKey-method | Has a feature a specific key? |
hasQualif | Has a feature a specific qualifier? |
hasQualif-method | Has a feature a specific qualifier? |
header | Extract the header from a '"gbRecord"' object. |
header-method | Extract the header from a '"gbRecord"' object. |
index | Access the indices of GenBank features |
index-method | Access the indices of GenBank features |
joint_range | Get the span of genomic features. |
joint_range-method | Get the span of genomic features. |
key | Get/set keys of GenBank features |
key-method | Get/set keys of GenBank features |
key<- | Get/set keys of GenBank features |
key<--method | Get/set keys of GenBank features |
length-method | Get the number of gbFeatures. |
loadRecord | Save and load 'gbRecord' objects. |
location | Access genomic locations of GenBank features |
location-method | Access genomic locations of GenBank features |
locusTag | Return the _locus_tag_ qualifiers from GenBank features. |
new_gbRecord | Class '"gbRecord"' |
note | Return the _note_ qualifiers from GenBank features. |
product | Return the _product_ qualifiers from GenBank features. |
proteinID | Return the _protein_id_ qualifiers from GenBank features. |
qualif | Get/set qualifiers of GenBank features |
qualif-method | Get/set qualifiers of GenBank features |
qualif<- | Get/set qualifiers of GenBank features |
qualif<--method | Get/set qualifiers of GenBank features |
qualifList | List the names of Genbank qualifiers. |
qualifList-method | List the names of Genbank qualifiers. |
qualifTable | Tabulate Genbank qualifiers |
qualifTable-method | Tabulate Genbank qualifiers |
ranges | Extract features as '"GRanges"' objects. |
ranges-method | Extract features as '"GRanges"' objects. |
revcomp | Reverse-complement features in a GenBank record |
revcomp-method | Reverse-complement features in a GenBank record |
saveRecord | Save and load 'gbRecord' objects. |
saveRecord-method | Save and load 'gbRecord' objects. |
select | Return a subset of features or annotations from a GenBank Record |
select-method | Return a subset of features or annotations from a GenBank Record |
shift | Shift the location of features in a GenBank record |
shift-method | Shift the location of features in a GenBank record |
span | Get the span of genomic features. |
span-method | Get the span of genomic features. |
start | Get or set the start position of genomic features |
start-method | Get or set the start position of genomic features |
start<- | Get or set the start position of genomic features |
start<--method | Get or set the start position of genomic features |
strand | Get or set the strand information of genomic features |
strand-method | Get or set the strand information of genomic features |
strand<- | Get or set the strand information of genomic features |
strand<--method | Get or set the strand information of genomic features |
summary | Summarise a GenBank record. |
summary-method | Summarise a GenBank record. |
translation | Return the _translation_s from GenBank features. |
uniqueQualifs | Quickly list all qualifier names. |
upstream | Find flanking features. |
write.FeatureTable | Write GenBank records or features to file in Feature Table format |
write.FeatureTable-method | Write GenBank records or features to file in Feature Table format |
write.GenBank | Write GenBank records or features to file in GenBank format |
write.GenBank-method | Write GenBank records or features to file in GenBank format |
$-method | Method extensions to extraction operator for gbRecord objects. |
[-method | Method extensions to extraction operator for gbRecord objects. |
[[-method | Method extensions to extraction operator for gbRecord objects. |