Files in markrobinsonuzh/Repitools
Epigenomic tools
.Rinstignore
DESCRIPTION
NAMESPACE
R/BAM2GRanges.R
R/ChromaBlocks.R
R/FastQC-class.R
R/GCadjustCopy.R
R/GCbiasPlots.R
R/abcdDNA.R
R/absoluteCN.R
R/annoDF2GR.R
R/annoGR2DF.R
R/annotationLookup.R
R/binPlots.R
R/blocksStats.R
R/checkProbes.R
R/chromosomeCNplots.R
R/classes.R
R/clusterPlots.R
R/cpgBoxplots.R
R/cpgDensityCalc.R
R/cpgDensityPlot.R
R/determineOffset.R
R/empBayes.R
R/enrichmentCalc.R
R/enrichmentPlot.R
R/featureBlocks.R
R/featureScores.R
R/findClusters.R
R/gcContentCalc.R
R/genQC.R
R/genomeBlocks.R
R/getProbePositionsDf.R
R/hyper.R
R/makeWindowLookup.R
R/mappabilityCalc.R
R/maskOut.R
R/mergeReplicates.R
R/methylEst.R
R/multiHeatmap.R
R/plotClusters.R
R/processNimblegenArrays.R
R/profilePlots.R
R/regionStats.R
R/relativeCN.R
R/sequenceCalc.R
R/summarizeScores.R
R/utils.R
R/writeWig.R
data/chr21genes.csv
data/datalist
data/expr.RData
data/hcRegions.RData
data/samplesList.RData
inst/CITATION
inst/examples/annotationCounts_seq.R
inst/examples/binPlots_affy.R
inst/examples/binPlots_seq.R
inst/examples/blockStats_affy.R
inst/examples/clusterPlots_seq.R
inst/examples/cpgDensityPlot_seq.R
inst/examples/enrichmentPlot_seq.R
inst/examples/featureScores_array.R
inst/examples/featureScores_seq.R
inst/examples/findClusters_dataframe.R
inst/examples/mergeReplicates_seq.R
inst/examples/regionStats_affy.R
man/AdjustedCopyEstimate-class.Rd
man/AffymetrixCdfFile-class.Rd
man/AffymetrixCelSet-class.Rd
man/BAM2GRanges.Rd
man/BayMethList-class.Rd
man/ChromaBlocks.Rd
man/ChromaResults-class.Rd
man/ClusteredScoresList-class.Rd
man/CopyEstimate-class.Rd
man/FastQC-class.Rd
man/GCAdjustParams-class.Rd
man/GCadjustCopy.Rd
man/GCbiasPlots.Rd
man/MappabilitySource-class.Rd
man/QdnaData.Rd
man/ScoresList-class.Rd
man/abcdDNA.Rd
man/absoluteCN.Rd
man/annoDF2GR.Rd
man/annoGR2DF.Rd
man/annotationBlocksCounts.Rd
man/annotationBlocksLookup.Rd
man/annotationCounts.Rd
man/annotationLookup.Rd
man/binPlots.Rd
man/blocksStats.Rd
man/checkProbes.Rd
man/chr21genes.Rd
man/chromosomeCNplots.Rd
man/clusterPlots.Rd
man/cpgBoxPlots.Rd
man/cpgDensityCalc.Rd
man/cpgDensityPlot.Rd
man/determineOffset.Rd
man/empBayes.Rd
man/enrichmentCalc.Rd
man/enrichmentPlot.Rd
man/expr.Rd
man/featureBlocks.Rd
man/featureScores.Rd
man/findClusters.Rd
man/gcContentCalc.Rd
man/genQC.Rd
man/genomeBlocks.Rd
man/getProbePositionsDf.Rd
man/getSampleOffsets.Rd
man/hcRegions.Rd
man/hyper.Rd
man/loadPairFile.Rd
man/loadSampleDirectory.Rd
man/makeWindowLookupTable.Rd
man/mappabilityCalc.Rd
man/maskOut.Rd
man/mergeReplicates.Rd
man/methylEst.Rd
man/multiHeatmap.Rd
man/plotClusters.Rd
man/plotQdnaByCN.Rd
man/processNDF.Rd
man/profilePlots.Rd
man/regionStats.Rd
man/relativeCN.Rd
man/samplesList.Rd
man/sequenceCalc.Rd
man/setCNVOffsets.Rd
man/summarizeScores.Rd
man/writeWig.Rd
src/Makevars
src/Makevars.win
src/Repitools.h
src/Rexchange.h
src/const.c
src/hyp2f1.c
src/mconf.h
src/mmeansd.cpp
src/mtherr.c
src/ringo_stuff.c
src/symbols.rds
tests/tests.R
vignettes/Repitools_vignette.Rnw
vignettes/analyses1.tex
vignettes/analyses2.tex
vignettes/clusterPlot.png
vignettes/datasets.tex
vignettes/qc-cpgPlot.pdf
vignettes/qc-enrPlot.pdf
vignettes/qc.tex
vignettes/readme.txt
vignettes/rock1.png
vignettes/sInfo.tex
vignettes/utilities.tex
vignettes/visualisations-binPlotsHeatmap.pdf
vignettes/visualisations-binPlotsLine.pdf
vignettes/visualisations-cluPlots3.pdf
vignettes/visualisations-profPlots.pdf
vignettes/visualisations.tex
