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.

Author
Daniel Fischer [aut, cre], Anu Sironen [aut]
Date of publication
2016-10-31 16:53:51
Maintainer
Daniel Fischer <daniel.fischer@luke.fi>
License
GPL (>= 2)
Version
0.9.2

View on CRAN

Man pages

blastSeq
Sending Genomic Sequences to NCBI Blast service
exportBed
Exporting a Bed File.
exportFA
Exporting a Fasta File.
findSpecies
Search in the 'species” Object.
getAnnotation
Downloading or Importing of Annotation Data
getEnsgInfo
Retrieve Gene Information From the NCBI Database.
getFastaFromBed
Get fasta information based on locations in bed-format
getGeneLocation
Extracting Gene Locations
getGeneSeq
Extracting a gene sequence from NCBI database.
hoardeR-package
Collect and Retrieve Annotation Data for Various Genomic Data...
importBed
Importing a Bed File.
importBlastTab
Import a Tab Delimited Blast Output File
importFA
Importing a Fasta File.
importXML
Import an XML File produced by the blastSeq function
intersectXMLAnnot
Intersect XML object with annotation object
plotHit
Visualization of a cross-species hit
print.fa
Print an fa Object
species
Available species at NCBI
subDose
Rewrite the Dose File from a Beagle Output
subGprobs
Rewrite the Gprobs File from a Beagle Output
subPhased
Rewrite the Phased File from a Beagle Output
summary.fa
Summarize an fa Object
tableSpecies
Tables the species in xml file
targetScan
Retrieving miRNA target information from targetscan.org

Files in this package

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