.getCache               Get BiocFileCache object
.getSummaryBam          Summarize BAM file
.singleAlignmentUMI4C   Align split fastq file
.singleCounterUMI4C     Count UMIs for a given bam file.
.singlePrepUMI4C        Prepar fastq files at a given barcode.
.singleSplitUMI4C       Split fastq files at a given restriction site.
.smoothMonotone         Monotone smoothing of the VST counts
UMI4C                   UMI4C-class
UMI4C2dds               UMI4Cats object to DDS object.
UMI4Cats                UMI4Cats: A package for analyzing UMI-4C
                        chromatin contact data
addGrouping             Add grouping of UMI-4C samples
addStepping             Add stepping for plotting genes
alignmentUMI4C          UMI4C alignment
calculateAdaptativeTrend
                        Adaptative smoothing of normalized trend
calculateDomainogram    Create Domainogram
callInteractions        Call significant interactions
combineUMI4C            Combine UMI4C fragments
contactsUMI4C           UMI4C Contacts Processing
counterUMI4C            UMI counting
createGeneAnnotation    Create gene annotation object
createStatsTable        Create stats table
darken                  Darken colors
dds2UMI4C               DDS object to UMI4Cats object.
demultiplexFastq        Demultiplex FASTQ files using fastq-multx
dgram                   UMI4C class methods
differentialNbinomWaldTestUMI4C
                        Differential UMI4C contacts using DESeq2 Wald
                        Test
digestGenome            Digest reference genome
downloadUMI4CexampleData
                        Download UMI4Cats example datasets
ex_ciita_umi4c          Contacts with CIITA promoter
fisherUMI4C             Differential UMI4C contacts using Fisher's
                        Exact test
formatPlotsUMI4C        Format plots for UMI4C
geoMeanCoordinates      Get geometric mean of given coordinates
getColors               Get default colors
getFactors              Get factors fro plotting
getNormalizationMatrix
                        Get normalization matrix
getSignInteractions     Get significant interactions from a GRangesList
getViewpointCoordinates
                        Get viewpoint coordinates
groupSamplesUMI4C       Group UMI4C samples
makeWindowFragments     Make windows merging restriction fragments
nbinomWaldTestUMI4C     Differential UMI4C contacts using DESeq2 Wald
                        Test
plotDifferential        Plot differential contacts
plotDomainogram         Plot domainogram
plotGenes               Plot genes
plotInteractions        Plot interactions
plotInteractionsUMI4C   Plot Interactions UMI4C
plotTrend               Plot adaptative smoothen trend
plotUMI4C               Plot UMI4C data
prepUMI4C               Prepare UMI4C data
smoothMonotoneUMI4C     Monotone smoothing of the DDS object VST counts
splitUMI4C              Split UMI4C reads
statsUMI4C              Statistics UMI4C
theme                   Theme
themeXYblank            Theme Y blank
themeXblank             Theme X blank
themeYblank             Theme Y blank
vstUMI4C                Variance stabilizing transformation
waldUMI4C               DESeq2 Wald test for differential contacts
zscoreUMI4C             Z-score calculation using residuals of trend
                        and fit UMI4C counts
