Yuanjian Huang

same issue, any suggestion?

Same issue, could you please tell me how you fix it @lindaseong @ghuls ? My pyscenic is version 0.12.0. I guess I should install the master release which was pulled...

Hello @ghuls `NameError: name 'gene_names' is not defined` happens when `arboreto_with_multiprocessing.py` is running in the Jupyter notebook in Windows. Is it able to fix this bug for Windows? I switched...

Hello @Sayyam-Shah Not developer. I believe that the GRNBOOST2 algorithm needs a revolution. It's low efficient now. In my case, 20000 cells with 20000 genes needs 150000 hours for running.

@Sa753 Could you please show me your folder contents in per_sample_outs folder? This is the example of our Cell Ranger outputs, but I don't remember the contents in subfolder of...

Hello Duanchen, Thanks for the response. However, your email address was not shown in the reply. Now, I found 2 genes that cannot be computed Scissor selected cells in my...

Hello Yuqi, Please check the following coding. Thanks! stPark = utils_loadObject("sampTab_Park_MouseKidney_062118.rda") > expPark = utils_loadObject("expMatrix_Park_MouseKidney_Oct_12_2018.rda") > dim(expPark) [1] 16272 43745 > [1] 16272 43745 Error: unexpected '[' in "[" >...

> Hi @YOU-k , currently I do not have a better suggestion on the generation of batch-corrected count matrix. Generally, we simply merge the data matrix from different batches and...

> > I have the same error > > Maybe you can change "as.matrix" in function "Scissor" as "as_matrix" ,like this: [as_matrix.txt](https://github.com/sunduanchen/Scissor/files/8357044/as_matrix.txt) [scissor_change.txt](https://github.com/sunduanchen/Scissor/files/8357045/scissor_change.txt) > > you can change the postfix...

@Miooooooo is correct. `Merge2.combined@graphs$RNA_snn=Merge2.combined@graphs$integrated_snn` plays the trick.