[](https://www.repostatus.org/#active)
[](https://codecov.io/github/UCLouvain-CBIO/scp?branch=master)
[](https://github.com/UCLouvain-CBIO/scp/actions?query=workflow%3AR-CMD-check-bioc)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/scp/)
[](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/).
