[results]downstream analysis of pyscenic using R like DE analysis

[jiangzh-coder]

For the downstream analysis of pyscenic, unfortunatelly, i do not found any tutorials using R script. What i want is to compare different conditions and different cell types, to find regulons which are condition and celltype specific. May i use wilcox test to analyze differences like DEGs analysis? i found 2 possible solutions as following, but i do not know if it is correct. Can anyone help me?

https://github.com/aet21/scira

https://saezlab.github.io/dorothea/articles/single_cell_vignette.html

[SeppeDeWinter]

Hi Jiangzh

Wilcoxon test is certainly a good option to explore differential regulons, we have used the same procedure here in the lab.

Also the package includes the Regulon Specificity Score (RSS) which scores each regulon for its specificity in different celltypes.

For the RSS analysis you can follow these tutorials:

• http://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/Tutorials_JupyterNotebooks/SCENIC_tutorial_2-ExploringOutput.html
• http://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html

Does this solve your problem?

Best,

Seppe

[jiangzh-coder]

Thanks lot, but it is for scenic. i need codes by R. thanks again

[SeppeDeWinter]

Both tutorials that I sent are in R. Or am I understanding your question wrongly?

Best,

Seppe

[SeppeDeWinter]

Closing due to inactivity, feel free to open again.

[yulchen810]

Hi, @SeppeDeWinter I'm wondering how to connect the output files(adjacencies, regulons, auc_mtx) from singularity/docker pyscenic with the scenicOptions object created by [scenicOptions <- initializeScenic(org="mgi", dbDir="cisTarget_databases", nCores=10)]. There is no tutorial for downstream analysis after container pyscenic process. If I miss any, please let me know.

Thank you! Best, Xiaoyan