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

Share:

Description

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

Value

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

Contact Information

We value all the feedback that we receive and will try to reply in a timely manner. Please report any bug that you encounter as well as any feature request that you may have to SNPhood@gmail.com.

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.