recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.
|Author||Panagiotis Moulos <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Panagiotis Moulos <email@example.com>|
|License||GPL (>= 3)|
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...
coverageRnaRef: Calculate coverage in a set of reference genomic regions...
getAnnotation: Annotation downloader
getBiotypes: List default Ensembl biotypes
kmeansDesign: Apply k-means clustering to profile data
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
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
simpleGetSet: Get and set some reusable objects from a recoup object
sliceObj: Subset recoup output list objects