KunHHE

Scyan statistical analysis?

1

Hi @quentinblampey, thanks for this message. I know the scyan package is mostly developed for cell type annotation and potential new cell population discovery. 1. May I ask if there...

reading .hdf5 file in sopa?

5

Hi @quentinblampey, Can I ask you if the case I have a .hdf5 file of the merscope AnnData (it has been segmented by cellpose but not annotated, and UMAPs are...

Hi @ziqlu0722, for Tangram run finished and got 'tangram_ct_pred', I don't feel confident for the downstream analysis step; can you help me a little? Thanks! For example, should I do...

ad_map data: var ('cell_type') added after the training in the merfish data frame, but it's 'NA'

4

Hi, I tried to run Tangram for cell type annotation. But don't know how Tangram works for cell type projection from reference data. I checked the ad_map, there's a var...

spatial operation analysis for visium hd compatible?

1

hi @quentinblampey, thanks again for this matter! may i ask you if we want to do spatial operation analysis using sopa, for visium hd data, does it compatible? especially the...

QC function?

1

Hi @JuliaS92 Thanks for developing the tool. May I ask you about the QC function in this package, before doing anything data processing? Thank you!

running time unlimited?

1

Hi @JuliaS92 Thanks for developing this tool. I noticed the running time is forever which is not normal I think? For example: ProteinGroups = pd.read_csv('C:/Users/hekun/Downloads/proteinGroupsDemo.txt',low_memory=False, sep = '\t') # ProteinGroups...

**Hi @sebastianbirk , tried to install this cool tool using HCP:** export TMPDIR=/lscratch/$SLURM_JOB_ID # keep all caches under /data/$USER (not /home) mkdir -p /data/$USER/.cache/pip \ /data/$USER/.cache \ /data/$USER/.conda/pkgs \ /data/$USER/.pycache...

C:\Users\username>baysor -v; but I got julia version 1.10.7?

1

Hi @VPetukhov, thanks fro your time on this issue. I installed GCC and julia, then the BAYSOR dependencies for sopa usage. using CLI: juliaup add 1.10; juliaup default 1.10; julia...

celltypist for Spatial transcriptmoic data (visium HD) annotation?

1

hi @ChuanXu1, can I ask you if celltypist model is ok for Spatial transcriptmoic data (visium HD) cell type annotation? For visium HD data, we always perform segmentation to assign...