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califano-lab / PISCES

R package for Protein activity analysis of single-cell RNAseq.
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Codes for generating ARANE network #4

Open LikaiTan opened 3 years ago

LikaiTan commented 3 years ago

Dear all, I am trying to apply the PISCES on my own scRNAseq data. However, I have been stuck about how to generate the ARACNe network in the same format as the cbmc-network you provided in the vignette. I can only generate something like below from my own data.

Regulator Target MI ATF1 FGFR1OP2 0.30649702815589475 ATF1 SCO1 0.17868938990992778 ATF1 FAR1 0.31422875152565677 ATF1 RNF219 0.18949220318012472 ATF1 ZNF24 0.2622082843634024 ATF1 PRELID3B 0.3526236748983633 ATF1 LARP4 0.3631380967164848 ATF1 MED17 0.3712452131481543 ATF1 PHF20L1 0.2714881972213714

It will be very nice if you can also provide the full script about how to generate the network from scRNAseq data.

Many thanks in advance.

Best, Likai

Huangbin8 commented 3 years ago

It can transform format by using aracne2regulon() of R package "viper".