UMI4Cats
This is the released version of UMI4Cats; for the devel version, see UMI4Cats.
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Bioconductor version: Release (3.23)
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.
Author: Mireia Ramos-Rodriguez [aut, cre] 
, Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]
Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at gmail.com>
citation("UMI4Cats")):Mireia Ramos-Rodriguez, Marc Subirana-Granes, Lorenzo Pasquali. UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data. doi:10.18129/B9.bioc.UMI4Cats, R package version 1.22.0, https://bioconductor.org/packages/UMI4Cats.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("UMI4Cats")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("UMI4Cats")| Analyzing UMI-4C data with UMI4Cats | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), SummarizedExperiment |
| Imports | magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics |
| System Requirements | |
| URL | https://github.com/Pasquali-lab/UMI4Cats |
| Bug Reports | https://github.com/Pasquali-lab/UMI4Cats/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat |
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| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | UMI4Cats_1.22.0.tar.gz |
| Windows Binary (x86_64) | UMI4Cats_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | UMI4Cats_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | UMI4Cats_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/UMI4Cats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/UMI4Cats |
| Package Short Url | https://bioconductor.org/packages/UMI4Cats/ |
| Package Downloads Report | Download Stats |