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Hello! Thank you so much for this package. I would like to run svds using the BPCells wrapper function on a matrix containing 9,096 genes and 4,188,533 cells. I followed the workflow outlined in the v…
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Hi, after check the parameters in sc.pl.umap, could you add a parameter 'legend_order' to customize legend order? Thanks.
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Hello everyone,
Thank you for this useful package. I am trying to follow the tutorial, but unfortunately it always turns me back an error, when I run this command:
IGAN2::plot_cellchat('PECAM1',…
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Thanks for sharing your dataset and code. I encounter some problems while running your analysis pipeline. Using the same random seed and code, I got 35 clusters after the whole "recursive Louvain clus…
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Hi,
Thank you for this great tool, it does allow much faster clustering of large datasets.
Using the default parameter, I get a very high number of clusters and I was wondering if there was a wa…
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This got published today: https://www.nature.com/articles/s41598-019-41695-z
A Java implementation is available at https://github.com/CWTSLeiden/networkanalysis.
I haven't looked at any of it in…
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hi,
i am trying to run your code in an ubuntu machine.
after compiling and packaging i tried the command louvian but i always get this error:
Error: Could not find or load main class com.sotera…
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Hey,
I just want to use the COVET method to compute niches on spatial data. I have several batches in my data. Should I just use `compute_covet` function with `batch_key` to get the `COVET_SQRT` re…
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Here are some of the features to (possibly) be included.
Priority:
- [x] Plot of gene expression per ROI
- [x] Differential gene expression analysis
- [x] Interactive plot (top DE genes)
- [x] …
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1. louvain property should not be in the config.
2. use = rather than contains for finding the node.
3. remove the LIMIT 1 in 2 places