realzehuali

[BUG]

3

When I was running: df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME, client_or_address = 'custom_multiprocessing', num_workers = 6) on my Windwos laptop with 64G RAM and 16 threads i7 CPU it turned out...

Relationship between TFs, receptors and ligands in new_ligand_receptor_TFs.txt

1

Thanks for the wonderful tool! This issue might only be about biology, not technology. In the file new_ligand_receptor_TFs.txt, there are 3 columns: Ligand_Symbol, Receptor_Symbol and TF_Symbol. In each row, is...

ValueError: After removing rows with only NaN interactions, none remain.

10

Following the same jupyter notebook (tutorial_visium_hne.ipynb) with the same tutorial data but got the following error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[10], line 6 1 sq.gr.ligrec( 2...

I noticed that the default method is paracrine. But I got more interactions when I chose the autocrine method. The data frame result of autocrine method could also include autocrine|paracrine....

write_matrix_dir does not write rownames and colnames of a matrix transformed from dgCMatrix

12

g = readRDS("raw.RDS") # previous Assay3 in dgCMatrix g[["RNA"]] = as(g[["RNA"]], Class = "Assay5") g[["RNA"]]$counts = as(g[["RNA"]]$counts, "IterableMatrix", strict = F) write_matrix_dir(mat = g[["RNA"]]$counts, dir = "BPCell/counts", overwrite = T)...