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 or SummarizedExperiment 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. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” Journal of Proteome Research 22 (9): 2775–84.

Vanderaa Christophe and Laurent Gatto. The current state of single-cell proteomics data analysis. Current Protocols 3 (1): e658.; doi: https://doi.org/10.1002/cpz1.658 (2023).

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

Contributions

Contributions are welcome, and should ideally be provdied through a Github pull request. Feel free to discuss any more non-trivial suggestions or changes first in an issue.

Contributors

• Micha Birklbauer: fix grep pattern in example for readSingleCellExperiment.