Package: genbankr 1.27.1

Gabriel Becker

genbankr: Parsing GenBank files into semantically useful objects

Reads Genbank files.

Authors:Gabriel Becker [aut, cre], Michael Lawrence [aut]

genbankr_1.27.1.tar.gz
genbankr_1.27.1.zip(r-4.5)genbankr_1.27.1.zip(r-4.4)genbankr_1.27.1.zip(r-4.3)
genbankr_1.27.1.tgz(r-4.4-any)genbankr_1.27.1.tgz(r-4.3-any)
genbankr_1.27.1.tar.gz(r-4.5-noble)genbankr_1.27.1.tar.gz(r-4.4-noble)
genbankr_1.27.1.tgz(r-4.4-emscripten)genbankr_1.27.1.tgz(r-4.3-emscripten)
genbankr.pdf |genbankr.html
genbankr/json (API)
NEWS

# Install 'genbankr' in R:
install.packages('genbankr', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/gmbecker/genbankr/issues

On CRAN:

24 exports 15 stars 1.95 score 70 dependencies

Last updated 9 months agofrom:cff319e721

Exports:accessioncdscdsBydefinitionexonsexonsByGBAccessionGenBankFilegenesgetSeqimportintergenicisCircularlocusmake_gbrecordmakeTxDbFromGenBankotherFeaturesparseGenBankreadGenBankseqinfosourcestranscriptsvariantsvers

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Annotation extraction apicds,GenBankRecord-method cdsBy,GenBankRecord cdsBy,GenBankRecord-method exons,GenBankRecord-method exonsBy,GenBankRecord exonsBy,GenBankRecord-method genes,GenBankRecord-method getSeq,GBAccession-method getSeq,GenBankFile-method getSeq,GenBankRecord-method isCircular,GenBankRecord isCircular,GenBankRecord-method seqinfo,GenBankRecord seqinfo,GenBankRecord-method transcripts,GenBankRecord-method
GBAccession ID classGBAccession GBAccession-class
genbankr specific apiaccession accession,GenBankRecord accession,GenBankRecord-method definition definition,GenBankRecord definition,GenBankRecord-method gbk-specific-api locus locus,GenBankRecord locus,GenBankRecord-method sources sources,GenBankRecord sources,GenBankRecord-method vers vers,GenBankRecord vers,GenBankRecord-method
GenBank FileGBFile-class GBKFile-class GenBankFile GenBankFile-class
GenBank data objectsGenBankRecord-class
Import genbank fileimport,GenBankFile import,GenBankFile,ANY,ANY-method
Extract intergenic regions from processed GenBank annotationsintergenic intergenic,GenBankRecord-method
GenBank object constructorsmake_gbrecord
Create a TxDb from a GenBank recordmakeTxDbFromGenBank makeTxDbFromGenBank,GBAccession makeTxDbFromGenBank,GBAccession-method makeTxDbFromGenBank,GenBankRecord makeTxDbFromGenBank,GenBankRecord-method
Retrieve 'other' featuresotherFeatures otherFeatures,GenBankRecord otherFeatures,GenBankRecord-method
Parse raw genbank file contentparseGenBank
Read a GenBank FilereadGenBank
Retrieve variantion featuresvariants variants,GenBankRecord variants,GenBankRecord-method