DOI: 10.18129/B9.bioc.UMI4Cats    

This is the development version of UMI4Cats; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.12)

UMI-4C is a technique that allows characterization of 3D chromatin contacts with a bait of interest. This package allows processing of UMI-4C data, starting with FASTQ files and finishing with statistical tests to call differential contacts in two conditions.

Author: Mireia Ramos-Rodriguez [aut, cre] , Marc Subirana-Granes [aut]

Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at>

Citation (from within R, enter citation("UMI4Cats")):


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biocViews Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 0.99.14
In Bioconductor since BioC 3.12 (R-4.0)
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
Suggests knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
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