:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-compartmap' .. highlight: bash bioconductor-compartmap ======================= .. conda:recipe:: bioconductor-compartmap :replaces_section_title: :noindex: Higher\-order chromatin domain inference in single cells from scRNA\-seq and scATAC\-seq :homepage: https://bioconductor.org/packages/3.17/bioc/html/compartmap.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-compartmap `_/`meta.yaml `_ Compartmap performs direct inference of higher\-order chromatin from scRNA\-seq and scATAC\-seq. This package implements a James\-Stein estimator for computing single\-cell level higher\-order chromatin domains. Further\, we utilize random matrix theory as a method to de\-noise correlation matrices to achieve a similar \"plaid\-like\" patterning as observed in Hi\-C and scHi\-C data. .. conda:package:: bioconductor-compartmap |downloads_bioconductor-compartmap| |docker_bioconductor-compartmap| :versions: .. raw:: html
1.18.0-01.16.0-01.12.0-01.10.0-01.8.0-11.8.0-01.6.0-01.4.0-01.2.0-1 ``1.18.0-0``,  ``1.16.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.0.2-0`` .. raw:: html
:depends bioconductor-biocsingular: ``>=1.16.0,<1.17.0`` :depends bioconductor-delayedarray: ``>=0.26.0,<0.27.0`` :depends bioconductor-delayedmatrixstats: ``>=1.22.0,<1.23.0`` :depends bioconductor-genomicranges: ``>=1.52.0,<1.53.0`` :depends bioconductor-hdf5array: ``>=1.28.0,<1.29.0`` :depends bioconductor-raggedexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-rtracklayer: ``>=1.60.0,<1.61.0`` :depends bioconductor-summarizedexperiment: ``>=1.30.0,<1.31.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ggplot2: :depends r-matrix: :depends r-reshape2: :depends r-rmtstat: :depends r-scales: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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-compartmap and update with:: mamba update bioconductor-compartmap To create a new environment, run:: mamba create --name myenvname bioconductor-compartmap 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 quay.io/biocontainers/bioconductor-compartmap: (see `bioconductor-compartmap/tags`_ for valid values for ````) .. |downloads_bioconductor-compartmap| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-compartmap.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-compartmap :alt: (downloads) .. |docker_bioconductor-compartmap| image:: https://quay.io/repository/biocontainers/bioconductor-compartmap/status :target: https://quay.io/repository/biocontainers/bioconductor-compartmap .. _`bioconductor-compartmap/tags`: https://quay.io/repository/biocontainers/bioconductor-compartmap?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-compartmap/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-compartmap/README.html