Givanna Putri

Following up on point 1 as I recently have had to deal with the disparate colour scales across different condition/group. I want the plots for each gene to have the...

> > I'm having the same issue converting an anndata h5ad that came from version 0.7.8. @JBreunig what version of anndata is your postdoc using? > > 0.7.6 and 1.8.1...

> Has CITE-seq support in scanpy been abandoned? Would you recommend muon instead? https://muon-tutorials.readthedocs.io/en/latest/cite-seq/1-CITE-seq-PBMC-5k.html You can still use the CLR transformation function provided in the previous posts to transform the...

@SamGG that's what I do now as a workaround. It's just a minor annoyance. Not an urgent bug to fix.

Feel free to try that approach and assess if it leads to any improvement. However, I suggest examining the `FlowSOM_cluster` column first, which provides the SOM node allocations for the...

You can increase the grid size by increasing the `xdim` and `ydim` parameter. Do note though that the size of the grid used by FlowSOM is `xdim` * `ydim`. Hence,...

oh i see what you mean now. I suppose that is one way of doing it, repeat `run.flowsom` and `run.umap` 3 times, each with different set of markers. By doing...

Hi @earbebarnes I just ran the install command u gave above and it seems to be working. There may have been issues with Github when u ran the command. Maybe...

> In my hands, the git repo results in a zip file named ImmuneDynamics-Spectre-v0.5.5-197-gd0fd33c.tar.gz of 234 MB. This is quite huge, IMHO, and may result in a large amount of...

Q1: Yes I would remove markers that are not present in the Fortessa. The markers have to exist in both datasets for the classification to work. Q2: I don't think...