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.

AuthorDaniel Fischer
Date of publication2016-12-31 17:21:51
MaintainerDaniel Fischer <daniel.fischer@luke.fi>
LicenseGPL (>= 2)
Version0.2.3

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

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

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.