zhanglab2008

Velocyto on single nucleus RNA-seq

3

Hi team, Thank you very much for developing this amazing tool! Do you think Velocyto is suitable for analyzing single nucleus RNA-seq dataset as well? The reason why I ask...

Inconsistent cell number in the json file and cell stats file

2

Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the zoom-in...

Dear @VPetukhov , If I don't like the default color in the :ncv_color column of the df_spatial DataFrame, how can I change it to a customized color palette? I really...

Install error in Ubuntu 20.04

1

Hi team, Congratulation on the new pipeline. However, I spent a day trying to install desc on my ubuntu server (20.04, amd64) but it failed. Here are my attempts: 1....

How to deal with the same barcodes when merging the bam files from multiple samples?

1

Hi Tim, Thanks for developing this tool! It's very handy. Just one question: If I want to merge the bam files from multiple samples after running ```sinto filterbarcodes```, how can...

Compare CCIs for more than two conditions

4

Hi team, I wonder if CrossTalkeR can be used to compare three conditions? Let's say, control, disease and treatment. Thanks!

multiThreads?

1

Hi really great work! I like UMAP.jl a lot. But when I run it on a matrix with a dimension of [400,000 x 30], it took about an hour to...

low mean but very significant

2

Hi team, Great work. I applied CellPhoneDB V2 on my dataset and got very meaningful result. Just one thing has puzzled me for a long time. In the Dot Plot,...

Hi Zhengtao, Very nice work! I was wondering if your metabolic scoring algorithm can be used to compare the metabolic activity across different conditions for the same cell type (let's...

Hi @bicycle1885 I tried your package and it worked quite good. Do you have any plans to register the package? That way people can easily install it by: ```]add Leiden```....