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GenomicTools (version 0.2.6)

Collection of Tools for Genomic Data Analysis

Description

A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.

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Version

Install

install.packages('GenomicTools')

Monthly Downloads

51

Version

0.2.6

License

GPL (>= 2)

Maintainer

Daniel Fischer

Last Published

July 11th, 2017

Functions in GenomicTools (0.2.6)

geneEXP

Simulated Expression Data
genotData

Simulated Genotype Data
annotTrack

Example Annotation Track
eQTL

Perform an eQTL Analysis
GenomicTools-package

Loose Collection of Expression and Genotype Analysis Tools, including (e)QTL and MDR.
QTL

Perform a QTL Analysis
getKEGGPathwayImage

Get a visualization of a specific KEGG pathway.
getKEGGPathwayOverview

Get a list of pathways in a specific organism.
getKEGGOrganisms

Get a list of organisms in the KEGG database
getKEGGPathway

Get a list of genes in a specific KEGG pathway.
importGFF3

Import a GFF3 File
importGTF

Import a GTF File
importPED

Import a Ped/Map filepair.
importSTARLog

Import a log-file from the STAR mapper.
phenoData

Simulated Phenotype Data
mdrEnsemble

Ensemble Classification Using an Existing MDR Object
mdrExample

Example Data for MDR
print.eqtl

Print an eqtl Object
print.mdr

Print an mdr Object
importVCF

Import a vcf file.
recodeData

Recode a Genotype Data Matrix.
summary.eqtl

Summarize an eqtl Object
plot.eqtl

Plot an eqtl Object
getRSLocation

Get the location of an SNP.
gtfToBed

Extract the Chromosomal Information Required in bed Format from an imported gtf table.
plot.mdr

Plot an MDR Object
plot.qtlRes

Plot an qtlRes Object
mdr

Perform a MDR.