GeneticTools: Collection of Genetic Data Analysis Tools

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A loose collection of tools for the analysis of gene expression and genotype data, currently with main focus on eQTL and MDR analysis.

Author
Daniel Fischer
Date of publication
2015-02-04 13:12:25
Maintainer
Daniel Fischer <daniel.fischer@luke.fi>
License
GPL (>= 2)
Version
0.3.1

View on CRAN

Man pages

annotTrack
Example Annotation Track
calcDistances
Calculate Distances Between Time Series
eQTL
Perform an eQTL Analysis
GeneticTools-package
GeneticTools
genotData
Simulated Genotype Data
genotypePlot
Expression Boxplots
getRegionsOI
Filter Annotation File
gtfToBed
Extract the Chromosomal Information Required in bed Format...
mdr
Perform a MDR.
plot.eqtl
Plot an eqtl Object
plot.mdr
Plot an MDR Object
predict.mdr
Calculates MDR Ensemble Classifier
print.eqtl
Print an eqtl Object
print.mdr
Print an mdr Object
realSNPs
Simulated SNP Data
recodeData
Recode a Genotype Data Matrix.
summary.eqtl
Summarize an eqtl Object
visTrans
Visualize trans-eQTL Results
Xgene
Simulated Expression Data

Files in this package

GeneticTools
GeneticTools/inst
GeneticTools/inst/ChangeLog
GeneticTools/ToDo
GeneticTools/src
GeneticTools/src/Makevars
GeneticTools/src/mdr.h
GeneticTools/src/timeCluster.h
GeneticTools/src/mdr.cpp
GeneticTools/src/timeCluster.cpp
GeneticTools/src/Makevars.win
GeneticTools/NAMESPACE
GeneticTools/data
GeneticTools/data/annotTrack.rda
GeneticTools/data/Xgene.rda
GeneticTools/data/realSNPs.rda
GeneticTools/data/genotData.rda
GeneticTools/R
GeneticTools/R/predict.mdr.R
GeneticTools/R/mdrEnsemble.R
GeneticTools/R/visTrans.R
GeneticTools/R/getRegionsOI.R
GeneticTools/R/joinEQTLsig.R
GeneticTools/R/print.eqtl.R
GeneticTools/R/rearrange.R
GeneticTools/R/plot.eqtl.R
GeneticTools/R/QTL.R
GeneticTools/R/gtfToBed.R
GeneticTools/R/makeannotList.R
GeneticTools/R/eqtlLM.R
GeneticTools/R/mdr.R
GeneticTools/R/recodeData.R
GeneticTools/R/plotGeneLocation.R
GeneticTools/R/calcDistances.R
GeneticTools/R/getSNPlocations.R
GeneticTools/R/print.mdrPredict.R
GeneticTools/R/cWrappers.R
GeneticTools/R/columnLabels.R
GeneticTools/R/genotypePlot.R
GeneticTools/R/eqtlDir.R
GeneticTools/R/eqtl.R
GeneticTools/R/summary.eqtl.R
GeneticTools/R/joinEQTL.R
GeneticTools/R/plot.mdr.R
GeneticTools/R/print.mdr.R
GeneticTools/vignettes
GeneticTools/vignettes/GeneticTools.tex
GeneticTools/vignettes/GeneticTools.pdf
GeneticTools/MD5
GeneticTools/DESCRIPTION
GeneticTools/man
GeneticTools/man/mdr.Rd
GeneticTools/man/getRegionsOI.Rd
GeneticTools/man/Xgene.Rd
GeneticTools/man/genotypePlot.Rd
GeneticTools/man/eQTL.Rd
GeneticTools/man/calcDistances.Rd
GeneticTools/man/print.eqtl.Rd
GeneticTools/man/visTrans.Rd
GeneticTools/man/annotTrack.Rd
GeneticTools/man/plot.mdr.Rd
GeneticTools/man/GeneticTools-package.Rd
GeneticTools/man/predict.mdr.Rd
GeneticTools/man/recodeData.Rd
GeneticTools/man/summary.eqtl.Rd
GeneticTools/man/realSNPs.Rd
GeneticTools/man/plot.eqtl.Rd
GeneticTools/man/genotData.Rd
GeneticTools/man/print.mdr.Rd
GeneticTools/man/gtfToBed.Rd