genbankr: Parsing GenBank files into semantically useful objects
Version 1.4.0

Reads Genbank files.

Browse man pages Browse package API and functions Browse package files

AuthorGabriel Becker [aut, cre], Michael Lawrence [aut]
Bioconductor views DataImport Infrastructure
Date of publicationNone
MaintainerGabriel Becker <becker.gabriel@gene.com>
LicenseArtistic-2.0
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("genbankr")

Man pages

api-methods: Annotation extraction api
GBAccession: GBAccession ID class
gbk-api: genbankr specific api
gbkfile: GenBank File
GenBank-classes: GenBank data objects
import: Import genbank file
intergenic: Extract intergenic regions from processed GenBank annotations
make_gbobjs: GenBank object constructors
otherFeatures: Retrieve 'other' features
parseGenBank: Parse raw genbank file content
readGenBank: Read a GenBank File
txdb: Create a TxDb from a GenBank record
variants: Retrieve variantion features

Functions

GBAccession Man page Source code
GBAccession-class Man page
GBFile-class Man page
GBKFile-class Man page
GenBankFile Man page Source code
GenBankFile-class Man page
GenBankRecord-class Man page
accession Man page
accession,GenBankRecord Man page
accession,GenBankRecord-method Man page
allna Source code
assignTxsToGenes Source code
cds,GenBankRecord-method Man page
cdsBy,GenBankRecord Man page
cdsBy,GenBankRecord-method Man page
chartxidToInt Source code
cheap_unsafe_data.frame Source code
chk_outer_complement Source code
definition Man page
definition,GenBankRecord Man page
definition,GenBankRecord-method Man page
do_join_silliness Source code
exons,GenBankRecord-method Man page
exonsBy,GenBankRecord Man page
exonsBy,GenBankRecord-method Man page
fastwriteread Source code
fill_stack_df Source code
gbk-specific-api Man page
genbanksum Source code
genes,GenBankRecord-method Man page
getGBfromNuccore Source code
getGeneIdLab Source code
getGeneIdVec Source code
getSeq,GBAccession-method Man page
getSeq,GenBankFile-method Man page
getSeq,GenBankRecord-method Man page
gnMappingHlpr Source code
import,GenBankFile Man page
import,GenBankFile,ANY,ANY-method Man page
intergenic Man page
intergenic,GenBankRecord-method Man page
isCircular,GenBankRecord Man page
isCircular,GenBankRecord-method Man page
locus Man page
locus,GenBankRecord Man page
locus,GenBankRecord-method Man page
makeTxDbFromGenBank Man page
makeTxDbFromGenBank,GBAccession Man page
makeTxDbFromGenBank,GBAccession-method Man page
makeTxDbFromGenBank,GenBankRecord Man page
makeTxDbFromGenBank,GenBankRecord-method Man page
make_cdsgr Source code
make_exongr Source code
make_feat_gr Source code
make_gbrecord Man page Source code
make_genegr Source code
make_txgr Source code
make_varvr Source code
match_cds_genes Source code
otherFeatures Man page
otherFeatures,GenBankRecord Man page
otherFeatures,GenBankRecord-method Man page
parseGenBank Man page Source code
readAccession Source code
readDefinition Source code
readFeatures Source code
readGenBank Man page Source code
readKeywords Source code
readLocus Source code
readOrigin Source code
readSource Source code
readVersions Source code
read_feat_attr Source code
seqTypeFromLocus Source code
seqinfo,GenBankRecord Man page
seqinfo,GenBankRecord-method Man page
simple_rbind_dataframe Source code
sources Man page
sources,GenBankRecord Man page
sources,GenBankRecord-method Man page
strip_feat_type Source code
strip_fieldname Source code
strip_outer_operator Source code
transcripts,GenBankRecord-method Man page
variants Man page
variants,GenBankRecord Man page
variants,GenBankRecord-method Man page
vers Man page
vers,GenBankRecord Man page
vers,GenBankRecord-method Man page

Files

CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R
R/api-methods.R
R/genbankReader.R
R/txdb.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/genbankr.R
inst/doc/genbankr.Rmd
inst/doc/genbankr.html
inst/examplefiles
inst/examplefiles/feat_del.txt
inst/examplefiles/test1.gbk
inst/sample.gbk
inst/unitTests
inst/unitTests/ABD64816.1.gpt
inst/unitTests/compjoin.gbk
inst/unitTests/locus_tag.gbk
inst/unitTests/multval.gbk
inst/unitTests/multval2.gbk
inst/unitTests/partial.gbk
inst/unitTests/test_set1.R
inst/unitTests/vars.gbk
man
man/GBAccession.Rd
man/GenBank-classes.Rd
man/api-methods.Rd
man/gbk-api.Rd
man/gbkfile.Rd
man/import.Rd
man/intergenic.Rd
man/make_gbobjs.Rd
man/otherFeatures.Rd
man/parseGenBank.Rd
man/readGenBank.Rd
man/txdb.Rd
man/variants.Rd
tests
tests/runTests.R
vignettes
vignettes/genbankr.Rmd
genbankr documentation built on May 20, 2017, 10:24 p.m.