:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-catalyst' .. highlight: bash bioconductor-catalyst ===================== .. conda:recipe:: bioconductor-catalyst :replaces_section_title: :noindex: Cytometry dATa anALYSis Tools :homepage: https://bioconductor.org/packages/3.18/bioc/html/CATALYST.html :license: GPL (>=2) :recipe: /`bioconductor-catalyst `_/`meta.yaml `_ CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS\, CyTOF\, and IMC. Preprocessing includes i\) normalization using bead standards\, ii\) single\-cell deconvolution\, and iii\) bead\-based compensation. For differential discovery\, the package provides a number of convenient functions for data processing \(e.g.\, clustering\, dimension reduction\)\, as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance \(DA\) and state \(DS\) analysis in order to identify differences in composition and expression profiles at the subpopulation\-level\, respectively. .. conda:package:: bioconductor-catalyst |downloads_bioconductor-catalyst| |docker_bioconductor-catalyst| :versions: .. raw:: html
1.26.0-01.24.0-01.22.0-01.18.0-01.16.0-01.14.0-11.14.0-01.12.1-01.10.0-0 ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.8.6-0``,  ``1.6.0-0`` .. raw:: html
:depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-consensusclusterplus: ``>=1.66.0,<1.67.0`` :depends bioconductor-flowcore: ``>=2.14.0,<2.15.0`` :depends bioconductor-flowsom: ``>=2.10.0,<2.11.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-scater: ``>=1.30.0,<1.31.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-circlize: :depends r-cowplot: :depends r-data.table: :depends r-dplyr: :depends r-drc: :depends r-ggplot2: :depends r-ggrepel: :depends r-ggridges: :depends r-gridextra: :depends r-matrix: :depends r-matrixstats: :depends r-nnls: :depends r-purrr: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rtsne: :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-catalyst and update with:: mamba update bioconductor-catalyst To create a new environment, run:: mamba create --name myenvname bioconductor-catalyst 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-catalyst: (see `bioconductor-catalyst/tags`_ for valid values for ````) .. |downloads_bioconductor-catalyst| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-catalyst.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-catalyst :alt: (downloads) .. |docker_bioconductor-catalyst| image:: https://quay.io/repository/biocontainers/bioconductor-catalyst/status :target: https://quay.io/repository/biocontainers/bioconductor-catalyst .. _`bioconductor-catalyst/tags`: https://quay.io/repository/biocontainers/bioconductor-catalyst?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-catalyst/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-catalyst/README.html