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[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](]( [![](]( [![R-CMD-check-bioc](]( [![Bioconductor-devel Build Status](]( [![license](]( # 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. <img src="" height="150"> ## Installation To install the **stable version** from Bioconductor: ```r 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. ```r BiocManager::install(version = "devel") stopifnot(BiocManager::valid()) ``` Then, you can install `scp` from Github. ```r 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: (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](