:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-linnorm' .. highlight: bash bioconductor-linnorm ==================== .. conda:recipe:: bioconductor-linnorm :replaces_section_title: :noindex: Linear model and normality based normalization and transformation method \(Linnorm\) :homepage: https://bioconductor.org/packages/3.18/bioc/html/Linnorm.html :license: MIT + file LICENSE :recipe: /`bioconductor-linnorm `_/`meta.yaml `_ Linnorm is an algorithm for normalizing and transforming RNA\-seq\, single cell RNA\-seq\, ChIP\-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods \(https\:\/\/doi.org\/10.1038\/s41592\-019\-0425\-8\). Linnorm can work with raw count\, CPM\, RPKM\, FPKM and TPM. .. conda:package:: bioconductor-linnorm |downloads_bioconductor-linnorm| |docker_bioconductor-linnorm| :versions: .. raw:: html
2.26.0-02.24.1-02.22.0-12.22.0-02.18.0-22.18.0-12.18.0-02.16.0-02.14.0-1 ``2.26.0-0``,  ``2.24.1-0``,  ``2.22.0-1``,  ``2.22.0-0``,  ``2.18.0-2``,  ``2.18.0-1``,  ``2.18.0-0``,  ``2.16.0-0``,  ``2.14.0-1``,  ``2.14.0-0``,  ``2.12.0-0``,  ``2.10.0-0``,  ``2.8.0-1``,  ``2.8.0-0``,  ``2.6.1-0``,  ``2.6.0-0`` .. raw:: html
:depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-amap: :depends r-apcluster: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ellipse: :depends r-fastcluster: :depends r-fpc: :depends r-ggdendro: :depends r-ggplot2: :depends r-gmodels: :depends r-igraph: :depends r-mass: :depends r-mclust: :depends r-rcpp: ``>=0.12.2`` :depends r-rcpparmadillo: ``>=0.8.100.1.0`` :depends r-rtsne: :depends r-statmod: :depends r-vegan: :depends r-zoo: :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-linnorm and update with:: mamba update bioconductor-linnorm To create a new environment, run:: mamba create --name myenvname bioconductor-linnorm 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-linnorm: (see `bioconductor-linnorm/tags`_ for valid values for ````) .. |downloads_bioconductor-linnorm| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-linnorm.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-linnorm :alt: (downloads) .. |docker_bioconductor-linnorm| image:: https://quay.io/repository/biocontainers/bioconductor-linnorm/status :target: https://quay.io/repository/biocontainers/bioconductor-linnorm .. _`bioconductor-linnorm/tags`: https://quay.io/repository/biocontainers/bioconductor-linnorm?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-linnorm/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-linnorm/README.html