chlee-tabin
chlee-tabin
Hi, I am not in the developer team, but if I could chime in, I do not think that pseudotime analysis is yet supported by velocyto nor scvelo, although I...
Just if I could chime in, I think https://github.com/satijalab/seurat-wrappers has what you need, and which I am using (I am not starting from .loom file, but essentially it requires only...
I may not be following, but "renaming the emat and nmat colnames" should be ``` colnames(emat)
Hi, I am not the developer but I have been working with dropEst with inDrop V3 dataset, and I think for dropTag, there is in dropEst/configs/indrop_v3_with_barcodes.xml that could be used....
@edroaldo Honestly, I trimmed the script for clarity, but essentially I copy pasted three times (not 15 times) to have the same droptag command with L001 to L002 etc... R1-R4...
JFYI, I am using the following 10x_v3.xml to process all my 10x v3 datasets which worked fine for me. I obtained it somewhere in the issue threads of this github....
Looks like the only difference between the 10x.xml and 10x_v3.xml is to change the following: ``` diff 10x.xml 10x_v3.xml 8c8 < 10 --- > 12 ```
I just wanted to chime in to this matter if you don't mind; I recently discovered that when using -V option to produce the matrices for velocyto, some genes that...
See this: https://github.com/hms-dbmi/dropEst/issues/105#issuecomment-641490931
Hi I am trying out PHATE too and wondering whether there is any code snippet to identify branch points. Without it it is difficult to identify genes at each branches...