hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices
Version 0.9.2

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hoardeR")

Getting started

Package overview
An Introduction to hoardeR

Popular man pages

exportFA: Exporting a Fasta File.
getFastaFromBed: Get fasta information based on locations in bed-format
importFA: Importing a Fasta File.
importXML: Import an XML File produced by the blastSeq function
plotHit: Visualization of a cross-species hit
subDose: Rewrite the Dose File from a Beagle Output
subPhased: Rewrite the Phased File from a Beagle Output
See all...

All man pages Function index File listing

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

Functions

R/hoardeR-package Man page
adjustCHRLabel Source code
blastSeq Man page Source code
cap Source code
createSpecies Source code
exportBed Man page Source code
exportFA Man page Source code
extractTSinfo Source code
findSpecies Man page Source code
getAnnotation Man page Source code
getBlastResult Source code
getEnsgInfo Man page Source code
getFastaFromBed Man page Source code
getGeneLocation Man page Source code
getGeneName Source code
getGeneSeq Man page Source code
getInfo Source code
getSameOrder Source code
importBed Man page Source code
importBlastTab Man page Source code
importFA Man page Source code
importXML Man page Source code
intersectXMLAnnot Man page Source code
intersectXMLAnnot.internal Source code
lastElement Source code
mergeVectors Source code
mixVectors Source code
onLoad Source code
plotHit Man page Source code
print,fa-method Man page
print.fa Man page
removeRight Source code
secToTime Source code
sendFA Source code
species Man page
subDose Man page Source code
subGprobs Man page Source code
subPhased Man page Source code
substrRight Source code
summary,fa-method Man page
summary.blastRes Source code
summary.fa Man page Source code
tableSpecies Man page Source code
targetScan Man page Source code
timeStat Source code
timeToSec Source code

Files

inst
inst/ChangeLog
inst/doc
inst/doc/hoardeR-vignette.R
inst/doc/hoardeR-vignette.pdf
inst/doc/hoardeR-vignette.Rmd
NAMESPACE
data
data/species.rda
R
R/aaa.R
R/print.blastRes.R
R/subGProbs.R
R/intersectXMLAnnot.R
R/getEnsgInfo.R
R/subPhased.R
R/blastSeq.R
R/getFastaFromBed.R
R/sendFA.R
R/summary.blastRes.R
R/importBlastTab.R
R/importXML.R
R/helpFunctions.R
R/getGeneSeq.R
R/plotHit.R
R/getGeneLocation.R
R/importFA.R
R/createSpecies.R
R/importBed.R
R/subDose.R
R/exportBed.R
R/xxx.R
R/tableSpecies.R
R/getAnnotation.R
R/summary.fa.R
R/exportFA.R
R/findSpecies.R
R/targetScan.R
R/getBlastResult.R
R/print.fa.R
vignettes
vignettes/coverageExample.png
vignettes/pigFlanking.png
vignettes/hoardeR-vignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/findSpecies.Rd
man/plotHit.Rd
man/exportBed.Rd
man/print.fa.Rd
man/importBed.Rd
man/importFA.Rd
man/getGeneSeq.Rd
man/getEnsgInfo.Rd
man/subDose.Rd
man/importXML.Rd
man/blastSeq.Rd
man/summary.fa.Rd
man/hoardeR-package.Rd
man/getGeneLocation.Rd
man/getFastaFromBed.Rd
man/species.Rd
man/subPhased.Rd
man/exportFA.Rd
man/targetScan.Rd
man/intersectXMLAnnot.Rd
man/subGprobs.Rd
man/importBlastTab.Rd
man/getAnnotation.Rd
man/tableSpecies.Rd
hoardeR documentation built on May 19, 2017, 8:15 a.m.