:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-milor' .. highlight: bash bioconductor-milor ================== .. conda:recipe:: bioconductor-milor :replaces_section_title: :noindex: Differential neighbourhood abundance testing on a graph :homepage: https://bioconductor.org/packages/3.18/bioc/html/miloR.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-milor `_/`meta.yaml `_ Milo performs single\-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model. .. conda:package:: bioconductor-milor |downloads_bioconductor-milor| |docker_bioconductor-milor| :versions: ``1.10.0-0``,  ``1.8.1-0``,  ``1.6.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocneighbors: ``>=1.20.0,<1.21.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocsingular: ``>=1.18.0,<1.19.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :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-cowplot: :depends r-dplyr: :depends r-ggbeeswarm: :depends r-ggplot2: :depends r-ggraph: :depends r-ggrepel: :depends r-gtools: :depends r-igraph: :depends r-irlba: :depends r-matrix: ``>=1.3-0`` :depends r-matrixstats: :depends r-patchwork: :depends r-rcolorbrewer: :depends r-stringr: :depends r-tibble: :depends r-tidyr: :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-milor and update with:: mamba update bioconductor-milor To create a new environment, run:: mamba create --name myenvname bioconductor-milor 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-milor: (see `bioconductor-milor/tags`_ for valid values for ````) .. |downloads_bioconductor-milor| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-milor.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-milor :alt: (downloads) .. |docker_bioconductor-milor| image:: https://quay.io/repository/biocontainers/bioconductor-milor/status :target: https://quay.io/repository/biocontainers/bioconductor-milor .. _`bioconductor-milor/tags`: https://quay.io/repository/biocontainers/bioconductor-milor?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-milor/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-milor/README.html