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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