buildAnnotationDatabase | Build a local annotation database for recoup |
buildAnnotationStore | Build a local annotation database for recoup |
buildCustomAnnotation | Import custom annotation to the recoup annotation database... |
calcCoverage | Calculate coverages over a genomic region |
coverageRef | Calculate coverage in a set of reference genomic regions... |
coverageRnaRef | Calculate coverage in a set of reference genomic regions... |
getAnnotation | Annotation downloader |
getBiotypes | List default Ensembl biotypes |
getInstalledAnnotations | Load a recoup annotation element |
importCustomAnnotation | Import a recoup custom annotation element |
kmeansDesign | Apply k-means clustering to profile data |
loadAnnotation | Load a recoup annotation element |
mergeRuns | Merge recoup outputs of same type |
preprocessRanges | Read and preprocess BAM/BED files to GRanges |
profileMatrix | Calculate final profile matrices for plotting |
recoup | Create genomic signal profiles in predefined or custom areas... |
recoupCorrelation | Plot (faceted) average genomic coverage correlations |
recoup-defunct | Defunct functions in package 'recoup' |
recoup-deprecated | Deprecated functions in package 'recoup' |
recoupHeatmap | Plot genomic coverage heatmaps |
recoupPlot | Plot list objects returned by recoup |
recoupProfile | Plot (faceted) average genomic coverage profiles |
recoup_test_data | Reference and genomic sample regions for recoup testing |
removeData | Remove data from recoup list object |
rpMatrix | Reads per million profile matrices for plotting |
simpleGetSet | Get and set some reusable objects from a recoup object |
sliceObj | Subset recoup output list objects |
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