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

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Documentation for package ‘UMI4Cats’ version 1.0.1

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.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
contactsUMI4C UMI4C Contacts Processing
counterUMI4C UMI counting
createGeneAnnotation Create gene annotation object
createStatsTable Create stats table
darken Darken colors
demultiplexFastq Demultiplex FASTQ files using fastq-multx
deseq2UMI4C DDS object to UMI4Cats object.
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 Contacs 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
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
nbinomWaldTestUMI4C Differential UMI4C contacts using DESeq2 Wald Test
plotDifferential Plot differential contacts
plotDomainogram Plot domainogram
plotGenes Plot genes
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