Marwan comments

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                                            Marwan

Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'>

updaing anndata from 0.7.6 to anndata 0.8 solved it for me

comparing classic umap and topometry

Thanks a lot that is very helpful and inspiring. for 1- you are right i haven't scaled the genes for 2- i am was trying to understand if i compute...

Liana on pseduo bulk-sc data data

sorry if i wasn't clear again, my question is about generation the ligand-receptor interactions df for example simply here for a single cell data object : `li.mt.rank_aggregate(adata, groupby='celltype', expr_prop=0.1, verbose=True)`...

Liana on pseduo bulk-sc data data

Thank you very much for your response. In fact, I am trying to benchmark and compare the different results that come from computing the CCC (cell-cell communication) on single-cell or...

FATAL ERROR - [E:int32_t main(int32_t, char**)] Your VCF/BCF files and SAM/BAM/CRAM files have different ordering of chromosomes. SAM/BAM/CRAM file has 1 before 10, but VCF/BCF file has 1 after 10 terminate called after throwing an instance of 'pException' what(): Exception was thrown Aborted (core dumped)

i got the same error and i would like to know if i need to reorder only the header withi the vcf file to match the bam or also the...

Using continuous variables yield weird results.

Thanks a lot for your response, @johannesostner Actually it's not a matter of normalisation ,For example checking the effect of age( in years) as a continuous variable , I observe...