Package: genbankr 1.27.1
![](https://r-universe.dev/static/nobody.jpg)
Gabriel Becker
genbankr: Parsing GenBank files into semantically useful objects
Reads Genbank files.
Authors:
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')) |
Bug tracker:https://github.com/gmbecker/genbankr/issues
Last updated 11 months agofrom:cff319e721. Checks:ERROR: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | FAIL | Aug 15 2024 |
R-4.5-win | ERROR | Aug 15 2024 |
R-4.5-linux | ERROR | Aug 15 2024 |
R-4.4-win | ERROR | Aug 15 2024 |
R-4.4-mac | ERROR | Aug 15 2024 |
R-4.3-win | ERROR | Aug 15 2024 |
R-4.3-mac | ERROR | Aug 15 2024 |
Exports:accessioncdscdsBydefinitionexonsexonsByGBAccessionGenBankFilegenesgetSeqimportintergenicisCircularlocusmake_gbrecordmakeTxDbFromGenBankotherFeaturesparseGenBankreadGenBankseqinfosourcestranscriptsvariantsvers
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Annotation extraction api | cds,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 class | GBAccession GBAccession-class |
genbankr specific api | accession 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 File | GBFile-class GBKFile-class GenBankFile GenBankFile-class |
GenBank data objects | GenBankRecord-class |
Import genbank file | import,GenBankFile import,GenBankFile,ANY,ANY-method |
Extract intergenic regions from processed GenBank annotations | intergenic intergenic,GenBankRecord-method |
GenBank object constructors | make_gbrecord |
Create a TxDb from a GenBank record | makeTxDbFromGenBank makeTxDbFromGenBank,GBAccession makeTxDbFromGenBank,GBAccession-method makeTxDbFromGenBank,GenBankRecord makeTxDbFromGenBank,GenBankRecord-method |
Retrieve 'other' features | otherFeatures otherFeatures,GenBankRecord otherFeatures,GenBankRecord-method |
Parse raw genbank file content | parseGenBank |
Read a GenBank File | readGenBank |
Retrieve variantion features | variants variants,GenBankRecord variants,GenBankRecord-method |