wgao688

For some reason UCSC changed access privileges. You need to use this link instead now: https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes

Hi @dbdimitrov , Thanks for your quick response! Running this, importantly with a specific version of numpy installed first, resolved the issues: ``` !pip install numpy==1.26.0 liana==1.5.0 cell2cell decoupler omnipath...

Hi @KyriakisDimitrios , I'm wondering if you solved this issue since I am also experiencing the same issue despite the suggestions here. I have tried using an SCE and Seurat...

I am also having this same issue. It appears to be an ArchR issue -- for some reason the tile.mtx@elementMetadata is NULL when it should return the tile coordinates.

Hi @jcurrie7, your code worked for me. Thanks for your help!

Hi @jcurrie7 , were you able to get the downstream CellSpace command line to work? Mine is seg faulting. This is my output: `CellSpace -output data/CellSpace_embedding-var_tiles -cpMat data/CellSpace_cell_by_tile-counts.mtx -peaks data/CellSpace_var_tiles.fa...

Hi @venkan , I have this same issue. Did you find a solution to this?

Thanks Seppe and Gert, I will try the code above. I am working with about 300K peaks for 300,000 cells. Should I subset to the most highly variable peaks (e.g.,...

@ghuls I am trying to run `pycistopic topic_modeling create_mallet_corpus -i "binary_accessibility.mtx" -o "corpus.mallet"` but I am not seeing the `create_mallet_corpus` option available. Is there something wrong with my download of...

I am also running into the same issue, running the code from this tutorial: https://saezlab.github.io/liana/articles/liana_ortho.html