:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-umi4cats' .. highlight: bash bioconductor-umi4cats ===================== .. conda:recipe:: bioconductor-umi4cats :replaces_section_title: :noindex: UMI4Cats\: Processing\, analysis and visualization of UMI\-4C chromatin contact data :homepage: https://bioconductor.org/packages/3.14/bioc/html/UMI4Cats.html :license: Artistic-2.0 :recipe: /`bioconductor-umi4cats `_/`meta.yaml `_ 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. .. conda:package:: bioconductor-umi4cats |downloads_bioconductor-umi4cats| |docker_bioconductor-umi4cats| :versions: ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.1-0``,  ``1.0.0-0`` :depends bioconductor-annotate: ``>=1.72.0,<1.73.0`` :depends bioconductor-biocfilecache: ``>=2.2.0,<2.3.0`` :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0`` :depends bioconductor-biostrings: ``>=2.62.0,<2.63.0`` :depends bioconductor-bsgenome: ``>=1.62.0,<1.63.0`` :depends bioconductor-deseq2: ``>=1.34.0,<1.35.0`` :depends bioconductor-genomeinfodb: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicalignments: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicfeatures: ``>=1.46.0,<1.47.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-iranges: ``>=2.28.0,<2.29.0`` :depends bioconductor-org.hs.eg.db: ``>=3.14.0,<3.15.0`` :depends bioconductor-rbowtie2: ``>=2.0.0,<2.1.0`` :depends bioconductor-regioner: ``>=1.26.0,<1.27.0`` :depends bioconductor-rsamtools: ``>=2.10.0,<2.11.0`` :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0`` :depends bioconductor-shortread: ``>=1.52.0,<1.53.0`` :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :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: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-umi4cats and update with:: conda update bioconductor-umi4cats or use the docker container:: docker pull quay.io/biocontainers/bioconductor-umi4cats: (see `bioconductor-umi4cats/tags`_ for valid values for ````) .. |downloads_bioconductor-umi4cats| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-umi4cats.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-umi4cats :alt: (downloads) .. |docker_bioconductor-umi4cats| image:: https://quay.io/repository/biocontainers/bioconductor-umi4cats/status :target: https://quay.io/repository/biocontainers/bioconductor-umi4cats .. _`bioconductor-umi4cats/tags`: https://quay.io/repository/biocontainers/bioconductor-umi4cats?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-umi4cats/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-umi4cats/README.html