recipe bioconductor-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.

package bioconductor-umi4cats

(downloads) docker_bioconductor-umi4cats



depends bioconductor-annotate:


depends bioconductor-biocfilecache:


depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-bsgenome:


depends bioconductor-deseq2:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicalignments:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:




depends bioconductor-rbowtie2:


depends bioconductor-regioner:


depends bioconductor-rsamtools:


depends bioconductor-s4vectors:


depends bioconductor-shortread:


depends bioconductor-summarizedexperiment:


depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:


depends r-base:


depends r-cowplot:

depends r-dplyr:

depends r-fda:

depends r-ggplot2:

depends r-magick:

depends r-magrittr:

depends r-r.utils:

depends r-rappdirs:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rlang:

depends r-scales:

depends r-stringr:

depends r-zoo:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-umi4cats

and update with::

   mamba update bioconductor-umi4cats

To create a new environment, run:

mamba create --name myenvname bioconductor-umi4cats

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-umi4cats/tags`_ for valid values for ``<tag>``)

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