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


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Documentation for package ‘hoardeR’ version 0.9.2

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R/hoardeR-package Collect and Retrieve Annotation Data for Various Genomic Data Using Different Web Services.
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.
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-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