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hoardeR (version 0.9.2)

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

Description

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.

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Version

Install

install.packages('hoardeR')

Monthly Downloads

270

Version

0.9.2

License

GPL (>= 2)

Maintainer

Daniel Fischer

Last Published

October 31st, 2016

Functions in hoardeR (0.9.2)

getEnsgInfo

Retrieve Gene Information From the NCBI Database.

importBed

Importing a Bed File.

intersectXMLAnnot

Intersect XML object with annotation object

subGprobs

Rewrite the Gprobs File from a Beagle Output

importBlastTab

Import a Tab Delimited Blast Output File

subDose

Rewrite the Dose File from a Beagle Output

importFA

Importing a Fasta File.

importXML

Import an XML File produced by the blastSeq function

plotHit

Visualization of a cross-species hit

print.fa

Print an fa Object

species

Available species at NCBI

targetScan

Retrieving miRNA target information from targetscan.org

tableSpecies

Tables the species in xml file

summary.fa

Summarize an fa Object

subPhased

Rewrite the Phased File from a Beagle Output

getFastaFromBed

Get fasta information based on locations in bed-format

hoardeR-package

Collect and Retrieve Annotation Data for Various Genomic Data Using Different Web Services.

exportFA

Exporting a Fasta File.

blastSeq

Sending Genomic Sequences to NCBI Blast service

getGeneLocation

Extracting Gene Locations

findSpecies

Search in the species` Object.

exportBed

Exporting a Bed File.

getAnnotation

Downloading or Importing of Annotation Data

getGeneSeq

Extracting a gene sequence from NCBI database.