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Vivianstats / scINSIGHT

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02649-3
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Interest in the simulated data #6

Open XinyeZhao opened 2 years ago

XinyeZhao commented 2 years ago

Hi scINSIGHT team,

I'm wondering if it's possible for you to also open source the scripts of running the scDesign to generate the simulated data used in the paper? Since you mentioned in the paper that the parameters are obtained from two separate datasets, it'll be great to have the scripts as a reference if using other datasets to run scDesign.

Thanks!

Vivianstats commented 2 years ago

Hi Xinye,

The two real datasets used by scDesign are directly obtained from the following publications:

Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, et al.Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017; 8(1):1–12.

Chu L-F, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell rna-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol. 2016; 17(1):1–20.

The scDesign package is available at https://github.com/Vivianstats/scDesign

The simulated data is available at: https://rutgers.app.box.com/s/atwckw3rvmdels96whkqvjr38vf27tqg

Hope this helps.