:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-msstatstmt' .. highlight: bash bioconductor-msstatstmt ======================= .. conda:recipe:: bioconductor-msstatstmt :replaces_section_title: :noindex: Protein Significance Analysis in shotgun mass spectrometry\-based proteomic experiments with tandem mass tag \(TMT\) labeling :homepage: https://bioconductor.org/packages/3.18/bioc/html/MSstatsTMT.html :license: Artistic-2.0 :recipe: /`bioconductor-msstatstmt `_/`meta.yaml `_ The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry\-based proteomic experiments with tandem mass tag \(TMT\) labeling. It provides multiple functionalities\, including aata visualization\, protein quantification and normalization\, and statistical modeling and inference. Furthermore\, it is inter\-operable with other data processing tools\, such as Proteome Discoverer\, MaxQuant\, OpenMS and SpectroMine. .. conda:package:: bioconductor-msstatstmt |downloads_bioconductor-msstatstmt| |docker_bioconductor-msstatstmt| :versions: .. raw:: html
2.10.0-02.8.0-02.6.0-02.2.0-02.0.0-01.8.2-11.8.2-01.8.0-01.6.0-0 ``2.10.0-0``,  ``2.8.0-0``,  ``2.6.0-0``,  ``2.2.0-0``,  ``2.0.0-0``,  ``1.8.2-1``,  ``1.8.2-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.5-0``,  ``1.1.2-0``,  ``1.0.0-0`` .. raw:: html
:depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-msstats: ``>=4.10.0,<4.11.0`` :depends bioconductor-msstatsconvert: ``>=1.12.0,<1.13.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-checkmate: :depends r-data.table: :depends r-ggplot2: :depends r-lme4: :depends r-lmertest: :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-msstatstmt and update with:: mamba update bioconductor-msstatstmt To create a new environment, run:: mamba create --name myenvname bioconductor-msstatstmt 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-msstatstmt: (see `bioconductor-msstatstmt/tags`_ for valid values for ````) .. |downloads_bioconductor-msstatstmt| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-msstatstmt.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-msstatstmt :alt: (downloads) .. |docker_bioconductor-msstatstmt| image:: https://quay.io/repository/biocontainers/bioconductor-msstatstmt/status :target: https://quay.io/repository/biocontainers/bioconductor-msstatstmt .. _`bioconductor-msstatstmt/tags`: https://quay.io/repository/biocontainers/bioconductor-msstatstmt?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-msstatstmt/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-msstatstmt/README.html