DOI: 10.18129/B9.bioc.UMI4Cats    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see UMI4Cats.

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

Bioconductor version: 3.14

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>

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biocViews Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (1.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), SummarizedExperiment
Imports magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats,, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics
Suggests knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
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