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README.md
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![codecov.io](https://codecov.io/github/UCLouvain-CBIO/scp/coverage.svg?branch=master)](https://codecov.io/github/UCLouvain-CBIO/scp?branch=master) [![R-CMD-check-bioc](https://github.com/UCLouvain-CBIO/scp/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/UCLouvain-CBIO/scp/actions?query=workflow%3AR-CMD-check-bioc) [![Bioconductor-devel Build Status](https://bioconductor.org/shields/build/devel/bioc/scp.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/scp/) [![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0) # 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`](https://rformassspectrometry.github.io/QFeatures/) package to manage and process [`SingleCellExperiment`](http://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) objects. <img src="https://raw.githubusercontent.com/UCLouvain-CBIO/scp/master/sticker/sticker.png" 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: 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](https://github.com/UCLouvain-CBIO/scp/issues) or the [Bioconductor support site](https://support.bioconductor.org/) to ask question or report problems with `scp`. ## License The `scp` code is provided under a permissive [Artistic 2.0 license](https://opensource.org/licenses/Artistic-2.0). The documentation, including the manual pages and the vignettes, are distributed under a [CC BY-SA license](https://creativecommons.org/licenses/by-sa/2.0/).