hoardeR

R-package for information retrieval from various bioinformatic-related databases.

Installation

The package depends on quite a few libraries and it can be cumbersome to install them manually. The easiest way to install the latest version of the package is with the help of the devtools package like this

install.packages("devtools")
devtools::install_github("fischuu/hoardeR")

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Version

Install

install.packages('hoardeR')

Version

0.10

License

GPL (>= 2)

Maintainer

Daniel Fischer

Last Published

April 8th, 2024

Functions in hoardeR (0.10)

summary.fa

Summarize an fa Object

tableSpecies

Tables the species in xml file

species

Available species at NCBI

subPhased

Rewrite the Phased File from a Beagle Output

subDose

Rewrite the Dose File from a Beagle Output

subGprobs

Rewrite the Gprobs File from a Beagle Output

targetScan

Retrieving miRNA target information from targetscan.org

getSequenceFromNCBI

Extracts a sequence from the NCBI webpage

blastSeq

Sending Genomic Sequences to NCBI Blast service

getEnsgInfo

Retrieve Gene Information From the NCBI Database.

getAnnotation

Downloading or Importing of Annotation Data

getGeneLocation

Extracting Gene Locations

findSpecies

Search in the species` Object.

getGeneSeq

Extracting a gene sequence from NCBI database.

plotHit

Visualization of a cross-species hit

hoardeR-package

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

coverageDensity

Calculation of the coverage density

intersectXMLAnnot

Intersect XML object with annotation object

getFastaFromBed

Get fasta information based on locations in bed-format

print.fa

Print an fa Object

plotCoverage

Plots a coverage density object