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Hi,
I have a question about the usage of compareCluster function. Is it only meant to be used to compare gene sets between different experimental conditions in the same species. Or can it also be u…
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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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Dear GitHub Community, can anyone help me with the following problem, please?
We treated two different cell lines with our substance of interest (in triplicates) and had RNA sequencing analysis don…
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Hi All,
I am hoping to plot some gene sets using PlotSurface and use the smooth_span parameter to smooth the expression levels of the gene sets. However, it does not seem like the smoothing paramet…
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Hello team,
I am trying to run the following
`enriched_p = gp.enrich(gene_list=genes,
gene_sets=custom_pathways,
background=None,
…
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Hi,
I am going through your vignette.
I have error after I type command: pbmc_B = pbmc[,pbmc$cell.type.coarse %in% 'B']
Error:
Error in h(simpleError(msg, call)) :
error in evaluati…
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**Describe the solution you'd like**
Add functions to calculate semantic similarity between gene sets and plot in MDS, similar to `rrvgo` for C5 GO terms
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Some possible gene sets:
- [ ] disease genetic associations (human only)
- [ ] drug binding (human only)
- [ ] tissue expression (data mostly from Bgee, human and mouse)
- [ ] genetic locus (P4…
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We have discussed the possibility to implement a PheWas plot from credible sets.
This ticket will incorporate scoping of such visualisation, also taking into account the existing datasets and how we …
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Opening an issue because @lmsimp and I would like to add some updated marker sets to pRolocmarkers and are wondering the best way to go about doing this.
Our initial thoughts are to leave the curr…