# UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

## Documentation for package ‘UMI4Cats’ version 1.21.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

UMI4Cats-package | UMI4Cats: A package for analyzing UMI-4C chromatin contact data
.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
addGrouping | Add grouping of UMI-4C samples
addStepping | Add stepping for plotting genes
alignmentUMI4C | UMI4C alignment
bait | UMI4C class methods
bait-method | UMI4C class methods
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
dgram-method | UMI4C class methods
dgram<- | UMI4C class methods
dgram<--method | 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
groupsUMI4C | UMI4C class methods
groupsUMI4C-method | UMI4C class methods
groupsUMI4C<- | UMI4C class methods
groupsUMI4C<--method | UMI4C class methods
makeUMI4C | UMI4C-class
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
resultsUMI4C | UMI4C class methods
resultsUMI4C-method | UMI4C class methods
smoothMonotoneUMI4C | Monotone smoothing of the DDS object VST counts
splitUMI4C | Split UMI4C reads
statsUMI4C | Statistics UMI4C
theme | Theme
themeXblank | Theme X blank
themeXYblank | Theme Y blank
themeYblank | Theme Y blank
trend | UMI4C class methods
trend-method | UMI4C class methods
UMI4C | UMI4C-class
UMI4C-class | UMI4C-class
UMI4C-methods | UMI4C class methods
UMI4C2dds | UMI4Cats object to DDS object.
UMI4Cats | UMI4Cats: A package for analyzing UMI-4C chromatin contact data
vstUMI4C | Variance stabilizing transformation
waldUMI4C | DESeq2 Wald test for differential contacts
zscoreUMI4C | Z-score calculation using residuals of trend and fit UMI4C counts