SirKuikka

About the phasing options

2

Hi, I have a few questions related to the phasing options. 1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) >...

Hi, I have scRNA-seq data and I am using log2 fold changes as the gene-level stats. How should I filter the genes prior to FGSEA? I have all 36 000...

  Hi, So I have this converging trajectory and when I visualize it, I can't figure out how to make the pseudotime fit the milestone network. `dynplot::plot_dimred(converging_traj,dimred = dyndimred::dimred_mds(converging_traj$expression),color_cells...

t-SNE visualization of distance matrix

1

Hi, I wonder what you think about using t-SNE to visualize the tcrdist distance matrix. Can this be used to find clusters that are likely to recognize the same epitope....

Xenium read error

7

Hi, I am using spatialdata-io v0.3.0 and trying to read the data from the Xenium bundle with this command xenium_bundle_path = "/path/to/xenium/data" zarr_path = "/path/to/workdir" sdata = xenium(xenium_bundle_path) but I...