GenomicTools: Collection of Tools for Genomic Data Analysis

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

Install the latest version of this package by entering the following in R:
install.packages("GenomicTools")
AuthorDaniel Fischer
Date of publication2017-04-08 20:47:32 UTC
MaintainerDaniel Fischer <daniel.fischer@luke.fi>
LicenseGPL (>= 2)
Version0.2.4

View on CRAN

Functions

annotTrack Man page
eQTL Man page
geneEXP Man page
genotData Man page
gtfToBed Man page
importGFF3 Man page
importGTF Man page
importPED Man page
importSTARLog Man page
importVCF Man page
mdr Man page
mdrEnsemble Man page
mdrExample Man page
phenoData Man page
plot.eqtl Man page
plot,eqtl-method Man page
plot.mdr Man page
plot,mdr-method Man page
plot,qtl-method Man page
plot.qtlRes Man page
print.eqtl Man page
print,eqtl-method Man page
print.mdr Man page
print,mdr-method Man page
print-method Man page
QTL Man page
recodeData Man page
R/GenomicTools-package Man page
summary.eqtl Man page
summary,eqtl-method Man page
summary-method Man page

Files

inst
inst/ChangeLog
inst/doc
inst/doc/GenomicTools-Vignette.Rmd
inst/doc/GenomicTools-Vignette.R
inst/doc/GenomicTools-Vignette.pdf
src
src/Makevars
src/mdr.h
src/RegisterRoutines.c
src/timeCluster.h
src/mdr.cpp
src/timeCluster.cpp
src/Makevars.win
NAMESPACE
data
data/annotTrack.rda
data/phenoData.rda
data/geneEXP.rda
data/datalist
data/mdrExample.rda
data/genotData.rda
R
R/predict.mdr.R R/mdrEnsemble.R R/print.mdrEnsemble.R R/visTrans.R R/aaa.R R/print.vcf.R R/plot.qtlRes.R R/importGTF.R R/getRegionsOI.R R/importGFF3.R R/joinEQTLsig.R R/print.eqtl.R R/print.qtlRes.R R/rearrange.R R/plot.eqtl.R R/summary.mdr.R R/QTL.R R/gtfToBed.R R/makeannotList.R R/eqtlLM.R R/mdr.R R/summary.qtlRes.R R/recodeData.R R/importVCF.R R/plotGeneLocation.R R/importSTARLog.R R/getSNPlocations.R R/print.mdrPredict.R R/summary.PedMap.R R/cWrappers.R R/plot.eqtl.trans.R R/columnLabels.R R/print.PedMap.R R/genotypePlot.R R/eqtlDir.R R/eqtl.R R/summary.eqtl.R R/importPED.R R/joinEQTL.R R/plot.mdr.R R/print.mdr.R
vignettes
vignettes/transEQTL.png
vignettes/cisEQTL.png
vignettes/GenomicTools-Vignette.Rmd
vignettes/MDR.png
vignettes/GenomicTools-Vignette.bib
vignettes/QTL2.png
vignettes/QTL1.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/mdrEnsemble.Rd man/mdr.Rd man/QTL.Rd man/mdrExample.Rd man/importSTARLog.Rd man/plot.qtlRes.Rd man/importGFF3.Rd man/eQTL.Rd man/importGTF.Rd man/geneEXP.Rd man/importVCF.Rd man/print.eqtl.Rd man/annotTrack.Rd man/plot.mdr.Rd man/phenoData.Rd man/recodeData.Rd man/summary.eqtl.Rd man/plot.eqtl.Rd man/GenomicTools-package.Rd man/genotData.Rd man/importPED.Rd man/print.mdr.Rd man/gtfToBed.Rd
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Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.