Single cell replication package

This package contains a series of vignettes that reproduce published SCP data analyses. Emphasis is put on standardization of the workflows.

Prerequisites

All vignettes are pre-compiled and can be found on the website under the Articles tab.

The replication package can be installed with R >= 4.1 by running:

BiocManager::install("UCLouvain-CBIO/SCP.replication")

Replication of SCP data analyses

The currently available replication vignettes are listed below.

Replication of the SCoPE2 analysis (Specht et al. 2021)

Project tag: SCoPE2 Docker image: cvanderaa/scp_replication_docker:v1

Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, et al. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 2021;22: 50.

See also

Exploring the autoPOTS data (Liang et al. 2020)

Project tag: liang2020 Docker image: cvanderaa/scp_replication_docker:v1

Liang, Yiran, Hayden Acor, Michaela A McCown, Andikan J Nwosu, Hannah Boekweg, Nathaniel B Axtell, Thy Truong, Yongzheng Cong, Samuel H Payne, and Ryan T Kelly. 2020. “Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling.” Anal. Chem., December.2021, 93, 3, 1658–1666.

Replication of the hair-cell development analysis (Zhu et al. 2019, eLife)

Project tag: zhu2019EL Docker image: cvanderaa/scp_replication_docker:v1

Zhu, Ying, Mirko Scheibinger, Daniel Christian Ellwanger, Jocelyn F Krey, Dongseok Choi, Ryan T Kelly, Stefan Heller, and Peter G Barr-Gillespie. 2019. “Single-Cell Proteomics Reveals Changes in Expression During Hair-Cell Development.” Elife 8 (November).

Replication of the AML model analysis (Schoof et al. 2021)

Project tag: schoof2021 Docker image: cvanderaa/scp_replication_docker:v1

Schoof, Erwin M., Benjamin Furtwängler, Nil Üresin, Nicolas Rapin, Simonas Savickas, Coline Gentil, Eric Lechman, Ulrich auf Dem Keller, John E. Dick, and Bo T. Porse. 2021. “Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies.” Nature Communications 12 (1): 745679.

See also

Reproducing the multiplexed SCP analysis by Williams et al. 2020

Project tag: williams2020_tmt Docker image: cvanderaa/scp_replication_docker:v1

Williams, Sarah M., Andrey V. Liyu, Chia-Feng Tsai, Ronald J. Moore, Daniel J. Orton, William B. Chrisler, Matthew J. Gaffrey, et al. 2020. “Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics.” Analytical Chemistry 92 (15): 10588–96.

Replication of the nPOP analysis (Leduc et al. 2022)

Project tag: leduc2022 Docker image: cvanderaa/scp_replication_docker:v1

Leduc, Andrew, R. Gray Huffman, Joshua Cantlon, Saad Khan, and Nikolai Slavov. 2022. “Exploring Functional Protein Covariation across Single Cells Using nPOP.” bioRxiv. https://doi.org/10.1101/2021.04.24.441211.

See also

Replication of the plexDIA analysis (Derks et al. 2022)

Project tag: derks2022 Docker image: cvanderaa/scp_replication_docker:v1

Derks, Jason, Andrew Leduc, Georg Wallmann, R. Gray Huffman, Matthew Willetts, Saad Khan, Harrison Specht, Markus Ralser, Vadim Demichev, and Nikolai Slavov. 2022. “Increasing the Throughput of Sensitive Proteomics by plexDIA.” Nature Biotechnology, July, 2021.11.03.467007.

See also

Replication of the cell cycle state study (Brunner et al. 2021)

Project tag: brunner2022 Docker image: cvanderaa/scp_replication_docker:v1

Brunner, Andreas-David, Marvin Thielert, Catherine Vasilopoulou, Constantin Ammar, Fabian Coscia, Andreas Mund, Ole B. Hoerning, et al. 2022. “Ultra-High Sensitivity Mass Spectrometry Quantifies Single-Cell Proteome Changes upon Perturbation.” Molecular Systems Biology 18 (3): e10798.

See also

SCP data re-analysis using scplainer

The vignettes that demonstrated how to use scplainer to analyse various SCP data sets are listed below.

If you use scplainer for your research, please cite:

Vanderaa, Christophe, and Laurent Gatto. 2023. “Scplainer: Using Linear Models to Understand Mass Spectrometry-Based Single-Cell Proteomics Data.” bioRxiv. https://doi.org/10.1101/2023.12.14.571792.

scplainer: reanalysis of the plexDIA dataset (Derks et al. 2022)

Project tag: scplainer_derks2022 Docker image: NA

Derks, Jason, Andrew Leduc, Georg Wallmann, R. Gray Huffman, Matthew Willetts, Saad Khan, Harrison Specht, Markus Ralser, Vadim Demichev, and Nikolai Slavov. 2022. “Increasing the Throughput of Sensitive Proteomics by plexDIA.” Nature Biotechnology, July, 2021.11.03.467007.

See also

scplainer: reanalysis of the nPOP dataset (Leduc et al. 2022)

Project tag: scplainer_leduc2022 Docker image: NA

Leduc, Andrew, R. Gray Huffman, Joshua Cantlon, Saad Khan, and Nikolai Slavov. 2022. “Exploring Functional Protein Covariation across Single Cells Using nPOP.” bioRxiv. https://doi.org/10.1101/2021.04.24.441211.

See also

scplainer: reanalysis of the AML dataset (Schoof et al. 2021)

Project tag: scplainer_schoof2021 Docker image: NA

Schoof, Erwin M., Benjamin Furtwängler, Nil Üresin, Nicolas Rapin, Simonas Savickas, Coline Gentil, Eric Lechman, Ulrich auf Dem Keller, John E. Dick, and Bo T. Porse. 2021. “Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies.” Nature Communications 12 (1): 745679.

See also

scplainer: reanalysis of the macrophage activation dataset (Woo et al. 2022)

Project tag: scplainer_woo2022 Docker image: NA

Woo, Jongmin, Geremy C. Clair, Sarah M. Williams, Song Feng, Chia-Feng Tsai, Ronald J. Moore, William B. Chrisler, et al. 2022. “Three-Dimensional Feature Matching Improves Coverage for Single-Cell Proteomics Based on Ion Mobility Filtering.” Cell Systems 13 (5): 426–34.e4.

Reproduce the analyses locally

You can reproduce the analysis vignettes on your local machine using Docker. You must first install Docker. Then, pull the image from the DockerHub repository.

docker pull cvanderaa/scp_replication_docker:vX

As we’ll release more vignettes, we will release new image tags. Make sure to pull the correct version vX for the vignette you want to reproduce (cf sections above).

Then, you can start an Rstudio session within a Docker container using:

docker run \
    -e PASSWORD=bioc \
    -p 8787:8787 \
    -v `pwd`:/home/rstudio/SCP.replication/ \ 
    cvanderaa/scp_replication_docker:vX

Note you should use %CD% instead of pwd when using Windows.

Open your browser and go to http://localhost:8787. The USER is rstudio and the password is bioc. See the DockerHub repository for more detailed information on getting started with Docker.

Note to future self

Build the docker image

Commit all recent changes to SCP.replication and push to the GitHub repo. The docker image is built from the master branch of UCLouvain-CBIO/SCP.replication, so make sure all changes needed for building the new vignette are live on GitHub. This is also true for:

  • rformassspectrometry/QFeatures
  • UCLouvain-CBIO/scpdata
  • UCLouvain-CBIO/scp

A new docker image should be built every time we add a new vignette. If new dependencies are required, update the Dockerfile accordingly.

Then build the image (make sure to cd in the SCP.replication repo):

docker build -t cvanderaa/scp_replication_docker:vX .

Make sure to increment vX with the latest version. See the DockerHub repo for the latest tag. When complete, push the new image to DockerHub:

docker push cvanderaa/scp_replication_docker:vX

Compile the vignette

You can compile a new vignette or update an existing one using:

docker run -e PASSWORD=scp \
        -v `pwd`:/home/rstudio/SCP.replication/ \
        -it cvanderaa/scp_replication_docker:vX \
        R --quiet -e "setwd('SCP.replication');pkgdown::build_article('VIGNETTE_NAME')"

Make sure to adapt vX and VIGNETTE_NAME with the correct tag and the name of the vignette to add or update.

Build the website

When you’re done compiling the vignette(s), rebuild the website shell using:

make website_shell

Push the changes in docs/ to Github.

Citation

To cite the SCP.replication website in publications please use:

Vanderaa Christophe and Laurent Gatto. The current state of single-cell proteomics data analysis. arXiv:2210.01020; doi: https://doi.org/10.48550/arXiv.2210.01020 (2022).

Licence

All vignettes are distributed under a CC BY-SA licence licence.