:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-sctreeviz' .. highlight: bash bioconductor-sctreeviz ====================== .. conda:recipe:: bioconductor-sctreeviz :replaces_section_title: :noindex: R\/Bioconductor package to interactively explore and visualize single cell RNA\-seq datasets with hierarhical annotations :homepage: https://bioconductor.org/packages/3.18/bioc/html/scTreeViz.html :license: Artistic-2.0 :recipe: /`bioconductor-sctreeviz `_/`meta.yaml `_ scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA\-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The \`TreeIndex\` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The \`TreeViz\` class extends \`SummarizedExperiment\` and can performs quick aggregations on the count matrix defined by clusters. .. conda:package:: bioconductor-sctreeviz |downloads_bioconductor-sctreeviz| |docker_bioconductor-sctreeviz| :versions: ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.0.0-0`` :depends bioconductor-epivizr: ``>=2.32.0,<2.33.0`` :depends bioconductor-epivizrdata: ``>=1.30.0,<1.31.0`` :depends bioconductor-epivizrserver: ``>=1.30.0,<1.31.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-scater: ``>=1.30.0,<1.31.0`` :depends bioconductor-scran: ``>=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-clustree: :depends r-data.table: :depends r-digest: :depends r-ggplot2: :depends r-ggraph: :depends r-httr: :depends r-igraph: :depends r-matrix: :depends r-rtsne: :depends r-seurat: :depends r-sys: :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-sctreeviz and update with:: mamba update bioconductor-sctreeviz To create a new environment, run:: mamba create --name myenvname bioconductor-sctreeviz 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-sctreeviz: (see `bioconductor-sctreeviz/tags`_ for valid values for ````) .. |downloads_bioconductor-sctreeviz| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-sctreeviz.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-sctreeviz :alt: (downloads) .. |docker_bioconductor-sctreeviz| image:: https://quay.io/repository/biocontainers/bioconductor-sctreeviz/status :target: https://quay.io/repository/biocontainers/bioconductor-sctreeviz .. _`bioconductor-sctreeviz/tags`: https://quay.io/repository/biocontainers/bioconductor-sctreeviz?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-sctreeviz/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-sctreeviz/README.html