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I have a large list of >277 genes that I still need to check for paralogs
This is quite time confusing but I have a heuristic!
Could you extract the PANTHER families for these?
If a panther fa…
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When I run the HMRF example in Giotto, I met this question, I can't install it in my HPC, could you give me some recommendations? Thank you so much!
HMRF spatial genes
doHMRF(gobject =visium kidney,…
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Hey @sigven,
Hope all is well :-)
I was wondering if it's possible to run cancer gene rank: https://sigven.github.io/oncoEnrichR/articles/cancer_gene_rank.html
as a stand-alone function for…
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Hi,
Thanks for this useful tool! I tried to apply Cytocipher to my data but got an error in step `cc.tl.merge_clusters`
```py
Cell In[10], line 1
----> 1 cc.tl.merge_clusters(rna, new_anno, n_…
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Hi @evanpeikon
Thank you for sharing this analysis. Interestingly, I get similar numbers of cells and genes, but I don't transpose the AnnData object. I end up with nearly identical numbers of gen…
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CCI
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Thank you for creating a nice software!
I'm wondering if it makes sense to exclude genes with poor prediction accuracy from prediction model as it could be noisy information.
Do you have any idea?
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Hi,
I would like to display different types of genes when using gtf file. Is there any aproach to display different types with different colors? In another word, that means anything like the `color=b…
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Hello, thank you for such a great and elegant package for plotting gene clusters. I was wondering if it is possible to allow all clusters have the same scale so that genes of the same length in bp wil…
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When I did cNMF in spatial transcriptomics, in which the n_counts of one spot could be smaller than scRNA-seq cell. It usually encounter that I have to drop many spots, due to there is no highly varai…