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.