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.

Author
Daniel Fischer
Date of publication
2016-10-13 00:35:47
Maintainer
Daniel Fischer <daniel.fischer@luke.fi>
License
GPL (>= 2)
Version
0.2.2

View on CRAN

Man pages

annotTrack
Example Annotation Track
eQTL
Perform an eQTL Analysis
geneEXP
Simulated Expression Data
GenomicTools-package
Loose Collection of Expression and Genotype Analysis Tools,...
genotData
Simulated Genotype Data
gtfToBed
Extract the Chromosomal Information Required in bed Format...
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.
importVCF
Import a vcf file.
mdr
Perform a MDR.
mdrEnsemble
Ensemble Classification Using an Existing MDR Object
mdrExample
Example Data for MDR
phenoData
Simulated Phenotype Data
plot.eqtl
Plot an eqtl Object
plot.mdr
Plot an MDR Object
plot.qtlRes
Plot an qtlRes Object
print.eqtl
Print an eqtl Object
print.mdr
Print an mdr Object
QTL
Perform a QTL Analysis
recodeData
Recode a Genotype Data Matrix.
summary.eqtl
Summarize an eqtl Object

Files in this package

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