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

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Documentation for package ‘UMI4Cats’ version 1.19.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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