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

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Documentation for package ‘hoardeR’ version 0.10

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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hoardeR-package	Collect and Retrieve Annotation Data for Various Genomic Data Using Different Web Services.
blastSeq	Sending Genomic Sequences to NCBI Blast service
coverageDensity	Calculation of the coverage density
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.
getSequenceFromNCBI	Extracts a sequence from the NCBI webpage
intersectXMLAnnot	Intersect XML object with annotation object
plotCoverage	Plots a coverage density object
plotHit	Visualization of a cross-species hit
print-method	Print an fa Object
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-method	Summarize an fa Object
summary.fa	Summarize an fa Object
tableSpecies	Tables the species in xml file
targetScan	Retrieving miRNA target information from targetscan.org