Man pages for akdess/CaSpER
Identify large-scale CNV events from single cell or bulk RNA-Seq data
| assignStates | assignStates() |
| AverageReference | AverageReference() |
| calcROC | calcROC() |
| calculateLOHShiftsForEachSegment | calculateLOHShiftsForEachSegment() |
| casper | The CaSpER Class |
| CaSpER-package | CaSpER: Identify large-scale CNV events from single cell or... |
| CenterSmooth | CenterSmooth() |
| ControlNormalize | ControlNormalize() |
| CreateCasperObject | CreateCasperObject |
| extractEvents | extractEvents() |
| extractLargeScaleEvents | extractLargeScaleEvents() |
| extractMUAndCooccurence | extractMUAndCooccurence() |
| extractSegmentSummary | extractSegmentSummary() |
| gene.matrix | gene.matrix() |
| generateAnnotation | generateAnnotation() |
| generateEnrichmentSummary | generateEnrichmentSummary() |
| generateLargeScaleEvents | generateLargeScaleEvents() |
| generateParam | generateParam() |
| getDiffExprGenes | getDiffExprGenes() |
| goEnrichmentBP | goEnrichmentBP() |
| hello | Hello, World! |
| lohCallMedianFilter | lohCallMedianFilter() |
| lohCallMedianFilterByChr | readBAFExtractOutput() |
| mergeScalesAndGenerateFinalEventSummary | mergeScalesAndGenerateFinalEventSummary() |
| PerformMedianFilter | PerformMedianFilter() |
| PerformMedianFilterByChr | PerformMedianFilterByChr() |
| PerformSegmentationWithHMM | PerformSegmentationWithHMM() |
| plotBAFAllSamples | plotBAFAllSamples() |
| plotBAFInSeperatePages | plotBAFInSeperatePages() |
| plotBAFOneSample | plotBAFOneSample() |
| plotGEAllSamples | plotGEAllSamples() |
| plotGEAndBAFOneSample | plotGEAndBAFOneSample() |
| plotGEAndGT | plotGEAndGT() |
| plotHeatmap | plotHeatmap() |
| plotLargeScaleEvent | plotLargeScaleEvent() |
| plotLargeScaleEvent2 | plotLargeScaleEvent2() |
| plotMUAndCooccurence | plotMUAndCooccurence() |
| plotSCellCNVTree | plotSCellCNVTree() |
| plotSingleCellLargeScaleEventHeatmap | plotSingleCellLargeScaleEventHeatmap() |
| ProcessData | ProcessData() |
| readBAFExtractOutput | readBAFExtractOutput() |
| runCaSpER | runCaSpER() |
| splitByOverlap | splitByOverlap() |
