hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.

AuthorDaniel Fischer [aut, cre], Anu Sironen [aut]
Date of publication2016-10-31 16:53:51
MaintainerDaniel Fischer <daniel.fischer@luke.fi>
LicenseGPL (>= 2)
Version0.9.2

View on CRAN

Functions

blastSeq Man page
exportBed Man page
exportFA Man page
findSpecies Man page
getAnnotation Man page
getEnsgInfo Man page
getFastaFromBed Man page
getGeneLocation Man page
getGeneSeq Man page
importBed Man page
importBlastTab Man page
importFA Man page
importXML Man page
intersectXMLAnnot Man page
plotHit Man page
print.fa Man page
print,fa-method Man page
R/hoardeR-package Man page
species Man page
subDose Man page
subGprobs Man page
subPhased Man page
summary.fa Man page
summary,fa-method Man page
tableSpecies Man page
targetScan Man page

Files

hoardeR
hoardeR/inst
hoardeR/inst/ChangeLog
hoardeR/inst/doc
hoardeR/inst/doc/hoardeR-vignette.R
hoardeR/inst/doc/hoardeR-vignette.pdf
hoardeR/inst/doc/hoardeR-vignette.Rmd
hoardeR/NAMESPACE
hoardeR/data
hoardeR/data/species.rda
hoardeR/R
hoardeR/R/aaa.R hoardeR/R/print.blastRes.R hoardeR/R/subGProbs.R hoardeR/R/intersectXMLAnnot.R hoardeR/R/getEnsgInfo.R hoardeR/R/subPhased.R hoardeR/R/blastSeq.R hoardeR/R/getFastaFromBed.R hoardeR/R/sendFA.R hoardeR/R/summary.blastRes.R hoardeR/R/importBlastTab.R hoardeR/R/importXML.R hoardeR/R/helpFunctions.R hoardeR/R/getGeneSeq.R hoardeR/R/plotHit.R hoardeR/R/getGeneLocation.R hoardeR/R/importFA.R hoardeR/R/createSpecies.R hoardeR/R/importBed.R hoardeR/R/subDose.R hoardeR/R/exportBed.R hoardeR/R/xxx.R hoardeR/R/tableSpecies.R hoardeR/R/getAnnotation.R hoardeR/R/summary.fa.R hoardeR/R/exportFA.R hoardeR/R/findSpecies.R hoardeR/R/targetScan.R hoardeR/R/getBlastResult.R hoardeR/R/print.fa.R
hoardeR/vignettes
hoardeR/vignettes/coverageExample.png
hoardeR/vignettes/pigFlanking.png
hoardeR/vignettes/hoardeR-vignette.Rmd
hoardeR/MD5
hoardeR/build
hoardeR/build/vignette.rds
hoardeR/DESCRIPTION
hoardeR/man
hoardeR/man/findSpecies.Rd hoardeR/man/plotHit.Rd hoardeR/man/exportBed.Rd hoardeR/man/print.fa.Rd hoardeR/man/importBed.Rd hoardeR/man/importFA.Rd hoardeR/man/getGeneSeq.Rd hoardeR/man/getEnsgInfo.Rd hoardeR/man/subDose.Rd hoardeR/man/importXML.Rd hoardeR/man/blastSeq.Rd hoardeR/man/summary.fa.Rd hoardeR/man/hoardeR-package.Rd hoardeR/man/getGeneLocation.Rd hoardeR/man/getFastaFromBed.Rd hoardeR/man/species.Rd hoardeR/man/subPhased.Rd hoardeR/man/exportFA.Rd hoardeR/man/targetScan.Rd hoardeR/man/intersectXMLAnnot.Rd hoardeR/man/subGprobs.Rd hoardeR/man/importBlastTab.Rd hoardeR/man/getAnnotation.Rd hoardeR/man/tableSpecies.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.