Up: Components summary Author

Chiara Facciotto

Component Version Inputs Outputs Description
BSAlign 1.0 reference, reads, mates alignedReads Aligns BS or RRBS data though BSMAP software, version 2.74.
CellGrowthAssay 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
CombinationMatrix 1.0 in out, matrices, plots Compute the plate statistics for the plate survival assays and for dummy plates.
ControlsQCs 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
DiffMeth 1.0 rawFilteredNormMethyl, regions plots, differentialMethylation, visualization, analysis Function to compute differential methylation at a base/window/region resolution.
DSRTplots 1.0 in, annotations out, normalized, plots, combined, scores Plots the inhibition curves for each screening experiments, combine plots for different pretreatment times and computes the scores indicating the efficacy of each drug.
MethFilterNorm 1.0 methCallArray, groupIDs rawFilteredNormMethyl, statistics, analysis, visualization Function loading the methylation calls data into a MethylRaw or MethylRawList object (MethylKit package data types) and performing normalization and filtering of the data.
MethylCall 1.0 reference, alignment methylationCalling Perform Methylation Calling of aligned RRBS and WGBS data obtained from the component BSalign.
WARNING: It requires quite a big amount of CPU (For human genome, needs ~26GB memory or more).
PlateQCs 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
SelectDiffMeth 1.0 differentialMethylation, features signifDiffMeth, plots, annotation, visualization Function to select which bases/windows/regions are significantly differentially methylated.
SelectMethContext 1.0 methCall cpg, chg, chh, statistics Separate cytosines based on the methylation context in which they occur and produces statistics about context methylation.
SignificantCurves 1.0 in out, plots, auc Selects drugs based on their efficacy scores.

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