:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'bioconductor-limpa'
.. highlight: bash

bioconductor-limpa
==================

.. conda:recipe:: bioconductor-limpa
   :replaces_section_title:
   :noindex:

   Quantification and Differential Analysis of Proteomics Data

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/limpa.html
   :license: GPL (>=2)
   :recipe: /`bioconductor-limpa <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-limpa>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-limpa/meta.yaml>`_

   Quantification and differential analysis of mass\-spectrometry proteomics data\, with probabilistic recovery of information from missing values. Avoids the need for imputation. Estimates the detection probability curve \(DPC\)\, which relates the probability of successful detection to the underlying log\-intensity of each precursor ion\, and uses it to incorporate missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts precursor \(or peptide\) intensities including missing values and produces complete protein quantifications without the need for imputation. The uncertainty of the protein quantifications is propagated through to the limma analyses using variance modeling and precision weights\, ensuring accurate error rate control. The analysis pipeline can alternatively work with PTM or protein level data. The package name \"limpa\" is an acronym for \"Linear Models for Proteomics Data\".


.. conda:package:: bioconductor-limpa

   |downloads_bioconductor-limpa| |docker_bioconductor-limpa|

   :versions:
      
      

      ``1.2.5-0``

      

   
   :depends on bioconductor-limma: ``>=3.66.0,<3.67.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-data.table: 
   :depends on r-statmod: 

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-limpa

to add into an existing workspace instead, run::

    pixi add bioconductor-limpa

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-limpa

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-limpa

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/bioconductor-limpa:<tag>

(see `bioconductor-limpa/tags`_ for valid values for ``<tag>``).

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

.. _conda: https://conda.io
.. _pixi: https://pixi.sh
.. |downloads_bioconductor-limpa| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-limpa.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-limpa
   :alt:   (downloads)
.. |docker_bioconductor-limpa| image:: https://quay.io/repository/biocontainers/bioconductor-limpa/status
   :target: https://quay.io/repository/biocontainers/bioconductor-limpa
.. _`bioconductor-limpa/tags`: https://quay.io/repository/biocontainers/bioconductor-limpa?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-limpa";
        var versions = ["1.2.5"];
    </script>






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-limpa/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-limpa/README.html