recipe bioconductor-scp

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis






Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

package bioconductor-scp

(downloads) docker_bioconductor-scp



depends bioconductor-mscoreutils:


depends bioconductor-multiassayexperiment:


depends bioconductor-qfeatures:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-dplyr:

depends r-magrittr:

depends r-matrixstats:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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-scp

and update with::

   mamba update bioconductor-scp

To create a new environment, run:

mamba create --name myenvname bioconductor-scp

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<tag>

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

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