Package: UMI4Cats 1.23.0

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_1.23.0.tar.gz
UMI4Cats_1.23.0.zip(r-4.7)UMI4Cats_1.23.0.zip(r-4.6)UMI4Cats_1.23.0.zip(r-4.5)
UMI4Cats_1.23.0.tgz(r-4.6-any)UMI4Cats_1.23.0.tgz(r-4.5-any)
UMI4Cats_1.23.0.tar.gz(r-4.7-any)UMI4Cats_1.23.0.tar.gz(r-4.6-any)
UMI4Cats_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
UMI4Cats/json (API)

# Install 'UMI4Cats' in R:

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

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

Datasets:

ex_ciita_umi4c - Contacts with CIITA promoter

On BioConductor:UMI4Cats-1.23.0(bioc 3.24)UMI4Cats-1.22.0(bioc 3.23)

qualitycontrol preprocessing alignment normalization visualization sequencing coverage chromatin chromatin-interaction genomics umi4c

5.86 score 6 stars 12 scripts 41 exports 139 dependencies

Last updated from:b941a86040. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	299
linux-devel-x86_64	OK	558
source / vignettes	OK	469
linux-release-x86_64	OK	485
macos-release-arm64	OK	275
macos-oldrel-arm64	OK	378
windows-devel	OK	466
windows-release	OK	466
windows-oldrel	OK	491
wasm-release	OK	325

Exports:.UMI4C addGrouping alignmentUMI4C bait callInteractions combineUMI4C contactsUMI4C counterUMI4C createGeneAnnotation darken demultiplexFastq dgram dgram<-differentialNbinomWaldTestUMI4C digestGenome downloadUMI4CexampleData fisherUMI4C getSignInteractions getViewpointCoordinates groupsUMI4C groupsUMI4C<-makeUMI4C makeWindowFragments plotDifferential plotDomainogram plotGenes plotInteractions plotInteractionsUMI4C plotTrend plotUMI4C prepUMI4C resultsUMI4C splitUMI4C statsUMI4C theme themeXblank themeXYblank themeYblank trend UMI4C waldUMI4C

Dependencies:abind annotate AnnotationDbi ash askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli cluster codetools colorspace cowplot cpp11 crayon curl DBI dbplyr DelayedArray deldir DESeq2 deSolve dplyr farver fastmap fda fds filelock FNN formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hdrcde httr httr2 hwriter interp IRanges isoband jpeg jsonlite KEGGREST kernlab KernSmooth ks labeling lambda.r lattice latticeExtra lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime multicool mvtnorm nlme openssl pcaPP pillar pkgconfig plyr png pracma purrr pwalign R.methodsS3 R.oo R.utils R6 rainbow rappdirs Rbowtie2 RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl regioneR reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo ShortRead snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML xtable XVector yaml zoo

Analyzing UMI-4C data with UMI4Cats

Rendered fromUMI4Cats.Rmdusingknitr::rmarkdown

Last update: 2025-10-21
Started: 2020-06-12

Help page	Topics
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 samples	addGrouping
Add stepping for plotting genes	addStepping
UMI4C alignment	alignmentUMI4C
Adaptative smoothing of normalized trend	calculateAdaptativeTrend
Create Domainogram	calculateDomainogram
Call significant interactions	callInteractions
Combine UMI4C fragments	combineUMI4C
UMI4C Contacts Processing	contactsUMI4C
UMI counting	counterUMI4C
Create gene annotation object	createGeneAnnotation
Create stats table	createStatsTable
Darken colors	darken
DDS object to UMI4Cats object.	dds2UMI4C
Demultiplex FASTQ files using fastq-multx	demultiplexFastq
UMI4C class methods	bait 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 Test	differentialNbinomWaldTestUMI4C
Digest reference genome	digestGenome
Download UMI4Cats example datasets	downloadUMI4CexampleData
Contacts with CIITA promoter	ex_ciita_umi4c
Differential UMI4C contacts using Fisher's Exact test	fisherUMI4C
Format plots for UMI4C	formatPlotsUMI4C
Get geometric mean of given coordinates	geoMeanCoordinates
Get default colors	getColors
Get factors fro plotting	getFactors
Get normalization matrix	getNormalizationMatrix
Get significant interactions from a GRangesList	getSignInteractions
Get viewpoint coordinates	getViewpointCoordinates
Group UMI4C samples	groupSamplesUMI4C
Make windows merging restriction fragments	makeWindowFragments
Differential UMI4C contacts using DESeq2 Wald Test	nbinomWaldTestUMI4C
Plot differential contacts	plotDifferential
Plot domainogram	plotDomainogram
Plot genes	plotGenes
Plot interactions	plotInteractions
Plot Interactions UMI4C	plotInteractionsUMI4C
Plot adaptative smoothen trend	plotTrend
Plot UMI4C data	plotUMI4C
Prepare UMI4C data	prepUMI4C
Monotone smoothing of the DDS object VST counts	smoothMonotoneUMI4C
Split UMI4C reads	splitUMI4C
Statistics UMI4C	statsUMI4C
Theme	theme
Theme X blank	themeXblank
Theme Y blank	themeXYblank
Theme Y blank	themeYblank
UMI4C-class	.UMI4C makeUMI4C UMI4C UMI4C-class
UMI4Cats object to DDS object.	UMI4C2dds
UMI4Cats: A package for analyzing UMI-4C chromatin contact data	UMI4Cats-package UMI4Cats
Variance stabilizing transformation	vstUMI4C
DESeq2 Wald test for differential contacts	waldUMI4C
Z-score calculation using residuals of trend and fit UMI4C counts	zscoreUMI4C

Package: UMI4Cats 1.23.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)