This application has been tested on R >= 3.5.0, OSX 10.14 / Windows 7/8/10. R can be downloaded from the main R Project page or downloaded with the RStudio Application.
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Download all the data reports from the "search" section of MassIVE MSV000089159.
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Download the metadata file from the Supplemental file 4 of the paper or here at https://docs.google.com/spreadsheets/d/1JtkihjpyDzy3eamB2tLc6-YSjzENClQh/edit?usp=sharing&ouid=105737144695616543623&rtpof=true&sd=true.
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Create a new R project, and copy the .Rmd, .R, .py, and .txt files from the Code section (https://github.com/SlavovLab/nPOP) to it. There are several scrips related to preproccessing and full data set PCA (nPOP_Analysis_main.Rmd), cell cycle analysis (CDC.Rmd), melanoma subpopulation analysis (SubPOP.Rmd, and plexDIA/pSCoPE integrated analysis (plexDIA.R).
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Please update the file paths in the .Rmd scrips.
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Run!
The manuscript is freely available on bioRxiv: Leduc et al., 2022 (version 4). The peer reviewed version is available at Genome Biology: Leduc et al., 2022
Leduc, A., Huffman, R.G., Cantlon, J. et al. Exploring functional protein covariation across single cells using nPOP. Genome Biol 23, 261 (2022). https://doi.org/10.1186/s13059-022-02817-5
For more information, contact Slavov Laboratory.
The nPOP code is distributed by an MIT license.
Please feel free to contribute to this project by opening an issue or pull request.
For any bugs, questions, or feature requests, please use the GitHub issue system to contact the developers.