SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data


For more information and an introduction to the package, see the two vignettes.


Summary analyses and visualizations for the selected genomic regions with respect to, for example, their read counts, genotype, and allelic origin

SNPhood functions

analyzeSNPhood annotation annotationBins annotationBins2 annotationDatasets annotationReadGroups annotationRegions associateGenotypes collectFiles convertToAllelicFractions counts deleteDatasets deleteReadGroups deleteRegions enrichment getDefaultParameterList mergeReadGroups nBins nDatasets nReadGroups nRegions parameters plotAllelicBiasResults plotAllelicBiasResultsOverview plotAndCalculateCorrelationDatasets plotAndCalculateWeakAndStrongGenotype plotAndClusterMatrix plotBinCounts plotClusterAverage plotGenotypesPerCluster plotGenotypesPerSNP plotRegionCounts renameBins renameDatasets renameReadGroups renameRegions results testForAllelicBiases

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