:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-msimpute' .. highlight: bash bioconductor-msimpute ===================== .. conda:recipe:: bioconductor-msimpute :replaces_section_title: :noindex: Imputation of label\-free mass spectrometry peptides :homepage: https://bioconductor.org/packages/3.18/bioc/html/msImpute.html :license: GPL (>=2) :recipe: /`bioconductor-msimpute `_/`meta.yaml `_ MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR\/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low\-rank approximation of the underlying data matrix if they are MAR \(method \= \"v2\"\)\, by Barycenter approach if missingness is MNAR \(\"v2\-mnar\"\)\, or by Peptide Identity Propagation \(PIP\). .. conda:package:: bioconductor-msimpute |downloads_bioconductor-msimpute| |docker_bioconductor-msimpute| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-scran: ``>=1.30.0,<1.31.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-dplyr: :depends r-fnn: :depends r-matrixstats: :depends r-mvtnorm: :depends r-pdist: :depends r-reticulate: :depends r-softimpute: :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-msimpute and update with:: mamba update bioconductor-msimpute To create a new environment, run:: mamba create --name myenvname bioconductor-msimpute 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-msimpute: (see `bioconductor-msimpute/tags`_ for valid values for ````) .. |downloads_bioconductor-msimpute| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-msimpute.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-msimpute :alt: (downloads) .. |docker_bioconductor-msimpute| image:: https://quay.io/repository/biocontainers/bioconductor-msimpute/status :target: https://quay.io/repository/biocontainers/bioconductor-msimpute .. _`bioconductor-msimpute/tags`: https://quay.io/repository/biocontainers/bioconductor-msimpute?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-msimpute/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-msimpute/README.html