Single cell proteomics data processing

The scp package is used to process and analyse mass spectrometry-based single cell proteomics data. It relies on the QFeatures package to manage and process SingleCellExperiment objects.

Installation

To install the stable version from Bioconductor:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("scp")

To install the devel version from GitHub, you first need to ensure that you are using the devel release of Bioconductor and make sure your installed libraries are valid.

BiocManager::install(version = "devel")
stopifnot(BiocManager::valid())

Then, you can install scp from Github.

BiocManager::install("UCLouvain-CBIO/scp")

Citation

To cite the scp package in publications use:

Vanderaa Christophe and Laurent Gatto. Replication of Single-Cell Proteomics Data Reveals Important Computational Challenges. Expert Review of Proteomics, 1–9 (2021).

Vanderaa Christophe and Laurent Gatto. Replication of Single-Cell Proteomics Data Reveals Important Computational Challenges. bioRxiv 2021.04.12.439408; doi: https://doi.org/10.1101/2021.04.12.439408 (2021).

Asking for help

Feel free to use Github issues or the Bioconductor support site to ask question or report problems with scp.

License

The scp code is provided under a permissive Artistic 2.0 license. The documentation, including the manual pages and the vignettes, are distributed under a CC BY-SA license.