Man pages for Pasquali-lab/UMI4Cats
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

addGroupingAdd grouping of UMI-4C samples
addSteppingAdd stepping for plotting genes
alignmentUMI4CUMI4C alignment
calculateAdaptativeTrendAdaptative smoothing of normalized trend
calculateDomainogramCreate Domainogram
callInteractionsCall significant interactions
combineUMI4CCombine UMI4C fragments
contactsUMI4CUMI4C Contacts Processing
counterUMI4CUMI counting
createGeneAnnotationCreate gene annotation object
createStatsTableCreate stats table
darkenDarken colors
dds2UMI4CDDS object to UMI4Cats object.
demultiplexFastqDemultiplex FASTQ files using fastq-multx
differentialNbinomWaldTestUMI4CDifferential UMI4C contacts using DESeq2 Wald Test
digestGenomeDigest reference genome
dot-getCacheGet BiocFileCache object
dot-getSummaryBamSummarize BAM file
dot-singleAlignmentUMI4CAlign split fastq file
dot-singleCounterUMI4CCount UMIs for a given bam file.
dot-singlePrepUMI4CPrepar fastq files at a given barcode.
dot-singleSplitUMI4CSplit fastq files at a given restriction site.
dot-smoothMonotoneMonotone smoothing of the VST counts
downloadUMI4CexampleDataDownload UMI4Cats example datasets
ex_ciita_umi4cContacs with CIITA promoter
fisherUMI4CDifferential UMI4C contacts using Fisher's Exact test
formatPlotsUMI4CFormat plots for UMI4C
geoMeanCoordinatesGet geometric mean of given coordinates
getColorsGet default colors
getFactorsGet factors fro plotting
getNormalizationMatrixGet normalization matrix
getSignInteractionsGet significant interactions from a GRangesList
getViewpointCoordinatesGet viewpoint coordinates
groupSamplesUMI4CGroup UMI4C samples
makeWindowFragmentsMake windows merging restriction fragments
nbinomWaldTestUMI4CDifferential UMI4C contacts using DESeq2 Wald Test
pipePipe operator
plotDifferentialPlot differential contacts
plotDomainogramPlot domainogram
plotGenesPlot genes
plotInteractionsPlot interactions
plotInteractionsUMI4CPlot Interactions UMI4C
plotTrendPlot adaptative smoothen trend
plotUMI4CPlot UMI4C data
prepUMI4CPrepare UMI4C data
smoothMonotoneUMI4CMonotone smoothing of the DDS object VST counts
splitUMI4CSplit UMI4C reads
statsUMI4CStatistics UMI4C
themeTheme
themeXblankTheme X blank
themeXYblankTheme Y blank
themeYblankTheme Y blank
UMI4CUMI4C-class
UMI4C2ddsUMI4Cats object to DDS object.
UMI4CatsUMI4Cats: A package for analyzing UMI-4C chromatin contact...
UMI4C-methodsUMI4C class methods
vstUMI4CVariance stabilizing transformation
waldUMI4CDESeq2 Wald test for differential contacts
zscoreUMI4CZ-score calculation using residuals of trend and fit UMI4C...
Pasquali-lab/UMI4Cats documentation built on March 23, 2024, 9:42 p.m.