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
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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

On CRAN:

infrastructure dataimport

4.34 score 14 stars 39 scripts 24 exports 71 dependencies

Last updated 1 years agofrom:cff319e721. Checks:ERROR: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 13 2024
R-4.5-win	ERROR	Nov 13 2024
R-4.5-linux	ERROR	Nov 13 2024
R-4.4-win	ERROR	Nov 13 2024
R-4.4-mac	ERROR	Nov 13 2024
R-4.3-win	ERROR	Nov 13 2024
R-4.3-mac	ERROR	Oct 14 2024

Exports:accession cds cdsBy definition exons exonsBy GBAccession GenBankFile genes getSeq import intergenic isCircular locus make_gbrecord makeTxDbFromGenBank otherFeatures parseGenBank readGenBank seqinfo sources transcripts variants vers

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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