GG boy

how to use nichenet in cell development data

4

Hi, I have two development stage scRNA data, and I want to identify the improtant cell-cell interactions during the two stage. But I encounterd a problem that i cant define...

Hi, when I ran "the differential_nichenet_pEMT vignettes“，I found a warning in the step, code as follows, > exprs_sender_receiver % + inner_join(exprs_tbl_ligand, by = c("ligand")) %>% + inner_join(exprs_tbl_receptor, by = c("receptor"))...

Thank you for your awesome software! I got several errors in processing my smartseq3 data, and I have scanned some related_issues, yet it's not solved my problem. First, because several...

TypeError: Can't instantiate abstract class SCGEN with abstract methods setup_anndata

3

I have been trying to merge multiple single cell data using scgen recently, but when I tried to run the tutorial, an error occurred，as follows, --------------------------------------------------------------------------- TypeError Traceback (most recent...

to get a vairants list from GWAS catalog

3

Thanks you for this greate tool to access GWAS catalog datasets. I want to download the top associations SNPs from GWAS catalog, and convert it to a SNP variant list...

problem in intetpreting the SAMap integration results

2

Hello, Thank you for developing such a useful tool! I'm working on integrating scRNAseq data cross species, and with the samap tools, I got an integration result that looks pretty...

'export_pseudobulk' output difference log

1

Hi, I processed a batch of scATACseq data using pycistopic last year, at that time, the `export_pseudobulk` output in the juypter lab is as follows,  yet, When I was...

Thanks for your previous reply, I successfully completed the SCENT pipeline in multiome datasets included multiple celltypes. yet I have some questions about exploring and interpreting SCENT prediction results. I...

Hi, I installed the newest version to modifed p value confusion, yet there's a error in this version rGREAT. I didnt know what happened, and I ran rGREAT successfully in...

plot_rss problem

1

I used the old version scenic+ to build eGRN, but I met a problem when exploring eGRN results-plot rss, `plot_rss(scplus_obj, 'ACC_celltype.predicted_gene_based', num_columns=4, top_n=10,save = outDir + 'plots/regulon_specificity_scores.pdf')`  I found...