Package: UMI4Cats 1.17.0

Mireia Ramos-Rodriguez

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

UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.

Authors:Mireia Ramos-Rodriguez [aut, cre], Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]

UMI4Cats_1.17.0.tar.gz

UMI4Cats_1.17.0.tgz(r-4.4-any)UMI4Cats_1.17.0.tgz(r-4.3-any)
UMI4Cats_1.17.0.tar.gz(r-4.5-noble)UMI4Cats_1.17.0.tar.gz(r-4.4-noble)
UMI4Cats_1.17.0.tgz(r-4.4-emscripten)UMI4Cats_1.17.0.tgz(r-4.3-emscripten)
UMI4Cats.pdf |UMI4Cats.html✨
UMI4Cats/json (API)
NEWS

# Install 'UMI4Cats' in R:
install.packages('UMI4Cats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pasquali-lab/umi4cats/issues

Datasets:

On BioConductor:UMI4Cats-1.17.0(bioc 3.21)UMI4Cats-1.16.0(bioc 3.20)

qualitycontrolpreprocessingalignmentnormalizationvisualizationsequencingcoveragechromatinchromatin-interactiongenomicsumi4c

5.48 score 5 stars 7 scripts 158 downloads 41 exports 141 dependencies

Last updated 2 months agofrom:70163075fd. Checks:OK: 3 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:%>%addGroupingalignmentUMI4CbaitcallInteractionscombineUMI4CcontactsUMI4CcounterUMI4CcreateGeneAnnotationdarkendemultiplexFastqdgramdgram<-differentialNbinomWaldTestUMI4CdigestGenomedownloadUMI4CexampleDatafisherUMI4CgetSignInteractionsgetViewpointCoordinatesgroupsUMI4CgroupsUMI4C<-makeUMI4CmakeWindowFragmentsplotDifferentialplotDomainogramplotGenesplotInteractionsplotInteractionsUMI4CplotTrendplotUMI4CprepUMI4CresultsUMI4CsplitUMI4CstatsUMI4CthemethemeXblankthemeXYblankthemeYblanktrendUMI4CwaldUMI4C

Dependencies:abindannotateAnnotationDbiashaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcliclustercodetoolscolorspacecowplotcpp11crayoncurlDBIdbplyrDelayedArraydeldirDESeq2deSolvedplyrfansifarverfastmapfdafdsfilelockFNNformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehdrcdehttrhwriterinterpIRangesisobandjpegjsonliteKEGGRESTkernlabKernSmoothkslabelinglambda.rlatticelatticeExtralifecyclelocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemulticoolmunsellmvtnormnlmeopensslorg.Hs.eg.dbpcaPPpillarpkgconfigplogrplyrpngpracmapurrrpwalignR.methodsS3R.ooR.utilsR6rainbowrappdirsRbowtie2RColorBrewerRcppRcppArmadilloRcppEigenRCurlregioneRreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioczoo

Analyzing UMI-4C data with UMI4Cats

Mireia Ramos-Rodríguez and Marc Subirana-Granés

Rendered fromUMI4Cats.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-04-30
Started: 2020-06-12

Readme and manuals

Help Manual

Help pageTopics
Get BiocFileCache object.getCache
Summarize BAM file.getSummaryBam
Align split fastq file.singleAlignmentUMI4C
Count UMIs for a given bam file..singleCounterUMI4C
Prepar fastq files at a given barcode..singlePrepUMI4C
Split fastq files at a given restriction site..singleSplitUMI4C
Monotone smoothing of the VST counts.smoothMonotone
Add grouping of UMI-4C samplesaddGrouping
Add stepping for plotting genesaddStepping
UMI4C alignmentalignmentUMI4C
Adaptative smoothing of normalized trendcalculateAdaptativeTrend
Create DomainogramcalculateDomainogram
Call significant interactionscallInteractions
Combine UMI4C fragmentscombineUMI4C
UMI4C Contacts ProcessingcontactsUMI4C
UMI countingcounterUMI4C
Create gene annotation objectcreateGeneAnnotation
Create stats tablecreateStatsTable
Darken colorsdarken
DDS object to UMI4Cats object.dds2UMI4C
Demultiplex FASTQ files using fastq-multxdemultiplexFastq
UMI4C class methodsbait bait,UMI4C-method dgram dgram,UMI4C-method dgram<- dgram<-,UMI4C-method groupsUMI4C groupsUMI4C,UMI4C-method groupsUMI4C<- groupsUMI4C<-,UMI4C-method resultsUMI4C resultsUMI4C,UMI4C-method trend trend,UMI4C-method UMI4C-methods
Differential UMI4C contacts using DESeq2 Wald TestdifferentialNbinomWaldTestUMI4C
Digest reference genomedigestGenome
Download UMI4Cats example datasetsdownloadUMI4CexampleData
Contacs with CIITA promoterex_ciita_umi4c
Differential UMI4C contacts using Fisher's Exact testfisherUMI4C
Format plots for UMI4CformatPlotsUMI4C
Get geometric mean of given coordinatesgeoMeanCoordinates
Get default colorsgetColors
Get factors fro plottinggetFactors
Get normalization matrixgetNormalizationMatrix
Get significant interactions from a GRangesListgetSignInteractions
Get viewpoint coordinatesgetViewpointCoordinates
Group UMI4C samplesgroupSamplesUMI4C
Make windows merging restriction fragmentsmakeWindowFragments
Differential UMI4C contacts using DESeq2 Wald TestnbinomWaldTestUMI4C
Plot differential contactsplotDifferential
Plot domainogramplotDomainogram
Plot genesplotGenes
Plot interactionsplotInteractions
Plot Interactions UMI4CplotInteractionsUMI4C
Plot adaptative smoothen trendplotTrend
Plot UMI4C dataplotUMI4C
Prepare UMI4C dataprepUMI4C
Monotone smoothing of the DDS object VST countssmoothMonotoneUMI4C
Split UMI4C readssplitUMI4C
Statistics UMI4CstatsUMI4C
Themetheme
Theme X blankthemeXblank
Theme Y blankthemeXYblank
Theme Y blankthemeYblank
UMI4C-class.UMI4C makeUMI4C UMI4C UMI4C-class
UMI4Cats object to DDS object.UMI4C2dds
UMI4Cats: A package for analyzing UMI-4C chromatin contact dataUMI4Cats
Variance stabilizing transformationvstUMI4C
DESeq2 Wald test for differential contactswaldUMI4C
Z-score calculation using residuals of trend and fit UMI4C countszscoreUMI4C