where is the data of the file sc_nets?

[liu-zzu]

Hello,
When I run the R script singlecell_gex_viper_analysis.R, there is an error.
where is the data of the file sc_nets?
" filenames <- list.files("sc_nets/", pattern="Patient*", full.names=TRUE)"
Thanks !!!

[Aleksobrad]

sc_nets is the subdirectory available at https://github.com/Aleksobrad/single-cell-rcc-pipeline/tree/master/sc_nets

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On Fri, Jul 16, 2021 at 1:43 PM liu-zzu ***@***.***> wrote: Hello, When I run the R script singlecell_gex_viper_analysis.R, there is an error. where is the data of the file sc_nets? " filenames <- list.files("sc_nets/", pattern="Patient*", full.names=TRUE)" Thanks !!! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLHK2XOHRVCXEFWQOUIUVTTYBVUJANCNFSM5AP7SKUQ> .

[liu-zzu]

Thank you for your kind reply!
Between lines 1320 and 1340 in the R script “singlecell_gex_viper_analysis.R”, the code that generates the ARACNe network results seems to be missing there. Where is the code that generates the data in sc_nets file ?
Best wishes!

[Aleksobrad]

The code that generates the ARACNe networks is not implemented in R, and instead uses the java implementation of the ARACNe-AP tool from https://github.com/califano-lab/ARACNe-AP ARACNE is executed on the .rds files created in local environment by the makeCMFA() function within the R script. For each of these files ARACNe is run on our high-performance computing cluster to improve speed by parallelization. We describe this workflow in more detail at https://github.com/califano-lab/PISCES and in https://www.biorxiv.org/content/10.1101/2021.05.20.445002v2 We are working on future implementations of ARACNe executable directly from R, but at the moment ARACNe must be run separately within the overall workflow and requires a significant amount of compute time, or else a pre-computed set of ARACNe networks can be provided as input to downstream VIPER inferences.

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On Fri, Jul 16, 2021 at 10:58 PM liu-zzu ***@***.***> wrote: Thank you for your kind reply! Between lines 1320 and 1340 in the R script “singlecell_gex_viper_analysis.R”, the code that generates the ARACNe network results seems to be missing there. Where is the code that generates the data in sc_nets file ? Best wishes! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLHK2WM6VA4XYVARULS2ETTYDWWDANCNFSM5AP7SKUQ> .

[liu-zzu]

Thank you for your prompt reply！
Maybe you can set up a separate R script for parallel computing ARACNe network with library(parallel) in R。
Single-cell protein activity inference is very valuable work. And if it is easy to use, it would be universally welcomed.
Best wishes!

[baoyulinn]

Where is the Rscript "singlecell_gex_viper_analysis.R" ?
Thank you!

[Aleksobrad]

https://github.com/Aleksobrad/single-cell-rcc-pipeline/blob/master/singlecell_gex_viper_analysis.R

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On Mon, Sep 12, 2022 at 10:48 PM baoyulinn ***@***.***> wrote: Where is the Rscript "singlecell_gex_viper_analysis.R" ? Thank you! — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLHK2XB2GVIULXTKCMYFNTV57TPDANCNFSM5AP7SKUQ> . You are receiving this because you commented.Message ID: ***@***.***>