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| buildAnnotationStore | Build a local annotation database for recoup |
| calcCoverage | Calculate coverages over a genomic region |
| coverageRef | Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode) |
| coverageRnaRef | Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode) |
| getAnnotation | Annotation downloader |
| getBiotypes | List default Ensembl biotypes |
| getr | Get and set some reusable objects from a recoup object |
| kmeansDesign | Apply k-means clustering to profile data |
| 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 using short sequence reads |
| recoup-deprecated | Deprecated functions in package 'recoup' |
| recoupCorrelation | Plot (faceted) average genomic coverage correlations |
| 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 |
| setr | Get and set some reusable objects from a recoup object |
| sliceObj | Subset recoup output list objects |
| test.design | Reference and genomic sample regions for recoup testing |
| test.exons | Reference and genomic sample regions for recoup testing |
| test.genome | Reference and genomic sample regions for recoup testing |
| test.input | Reference and genomic sample regions for recoup testing |