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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Can I use GRNBoost output to SCENIC R pipline? #129

Closed lh12565 closed 2 years ago

lh12565 commented 4 years ago

Hi,

I use GRNBoost to infer a gene regulatory network. I want to use the output to further analysis in R as follows:

grnres<-read.table('grnboost_output.csv',stringsAsFactors=F,sep="\t")
saveRDS(grnres,"int/1.4_GENIE3_linkList.Rds")
runSCENIC_1_coexNetwork2modules(scenicOptions)
runSCENIC_2_createRegulons(scenicOptions) 
runSCENIC_3_scoreCells(scenicOptions, logMat)

But their column is different, so I changed the column "TF Target important" to "TF Target weight" as #40 said. I don't know is it correct to do this. And the GENIE3 weights are <1 while the GRNBoost importance range from 0-100+, so does this affect the results? I also see the pyscenic workflow, but I didn't find the motif database and I'm not familiar with python, so I use R to do the next step. Thanks!

morganee261 commented 4 years ago

Hi @lh12565, I am trying to import my pyscenic outputs into R to continue the analysis and am running into issues. Any luck with that?

thanks, Morgane

lh12565 commented 4 years ago

Hi @morganee261, I didn't use the pyscenic, and I only used grnboost (https://arboreto.readthedocs.io/en/latest/) to infer a gene regulatory network. What is your problem when you use the pyscenic?

millersan commented 4 years ago

I use this result like you show , I had run genie3 before in bulk data , the result is more likely grnboost . I succeed to get the final result .

luoboqingcai81 commented 4 years ago

i meet the same issue, the GENIE3 used in SCENIC is so slow. I used the GRNBoost in python, but the result is different from the GENIE3 in SCENIC

Chenmengpin commented 3 years ago

Hi,

I use GRNBoost to infer a gene regulatory network. I want to use the output to further analysis in R as follows:

grnres<-read.table('grnboost_output.csv',stringsAsFactors=F,sep="\t")
saveRDS(grnres,"int/1.4_GENIE3_linkList.Rds")
runSCENIC_1_coexNetwork2modules(scenicOptions)
runSCENIC_2_createRegulons(scenicOptions) 
runSCENIC_3_scoreCells(scenicOptions, logMat)

But their column is different, so I changed the column "TF Target important" to "TF Target weight" as #40 said. I don't know is it correct to do this. And the GENIE3 weights are <1 while the GRNBoost importance range from 0-100+, so does this affect the results? I also see the pyscenic workflow, but I didn't find the motif database and I'm not familiar with python, so I use R to do the next step. Thanks!

Hi, I meet the same issue like you described, did you get any answers? Thanks!

linxy29 commented 2 years ago

I also have the same problem and I'm seeking a solution.