Ayush Aggarwal comments

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                                            Ayush Aggarwal

FindTransferAnchors giving error when using an harmony integrated scRNA data as reference and spatial data as query

Thank you for your response @saketkc and @dcollins15. For now, I aggregated the two samples using cellranger and then performed clustering using seurat and batch correction using harmony giving me...

specifying chromosome does not map aliases if gene is correct on another chromosome

Sure. I'll fix it.

specifying chromosome does not map aliases if gene is correct on another chromosome

@lwaldron This issue was resolved in my last PR.

specifying chromosome does not map aliases if gene is correct on another chromosome

Yes, that I'm looking into but so far I've not been able to find the cause of that error. I'll check again.

specifying chromosome does not map aliases if gene is correct on another chromosome

Hi @lwaldron All the checks were passed in my last PR. This issue can be closed now.

Issue Running CONICSMat Tutorial Due To Deprecated SCRAN Function

Hi If anyone's still interested in the solution for this or comes looking for it in the future, they can use the below modified function to detect variable genes. detectVarGenes_custom...

Alias not mapped if gene is correct

Yes, this makes sense for the cases that I have presented. I was just worried about other such cases if present and also as the second reviewer mentioned, it could...

No output and intermediate file

Hi @dstyaaaaaa @CHAOYiming Were you able to figure out a solution for this? I'm also stuck at the same place and it says MT in both my bam and genome...

Mixscape NT classification

Hi, I got the same thing in my analysis. Some cells were labelled as NT in "mixscape_class.global" while they were NP in "mixscape_class". This only happened with gRNAs detected in...