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In the pipeline `v0.16.0`, using the following config:
```
clustering {
report_ipynb = '/src/scanpy/bin/reports/sc_clustering_report.ipynb'
methods = ['louvain']
…
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I'm sorry to refer to this closed issue again, but commenting out the two lines as in #41 `#adata.var['gene_id'] = adata.var['gene_id-1']`; `#adata.var.drop(columns = ['gene_id-1', 'gene_id-0'], inpla…
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Hi,
I am trying to apply the "Cell type classification using an integrated reference" from the Seurat Vignette
[https://satijalab.org/seurat/v3.2/integration.html](url)
I integrated 4 query Seu…
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Is it possible to use bipartite graphs? It is supported in the python version of the package so I wonder how one could implement it in the R version.
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Hi,
I found the article about FastPG very interesting and wanted to try it. But, I am not able to install FastPG using "Local install" method. I configured Python and installed nmslib as mentioned in…
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**Describe the bug**
Cannot install pyscenic==11.0 or pyscenic in conda environment. I made a fresh environemnt to install new version (11.0).
Outside of conda environment also, this is not being po…
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Hi Kristian
I hope it's ok I entertain you with questions regarding ex 10 ^^.
I've tried to implement the louvain method as outlined in ex 10.2. The returned community is not always the optimal …
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Hi.
I tried reproducing the example in comparison_to_kmeans.Rmd and for the most part it works well if I use bootstrap_type = "s" instead of "m" in k_fit_pch function (chunk #5). Otherwise I get the …
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Hi, I am confusing that I got different modularity in the same graph with different node labels. First, I got one modularity 0.382 in my network. Then I rename the node labels based on some sorted and…
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By default, singlelayer_louvain and multilayer_louvain return a tuple community membership vector at the moment.
Some scripts are using the return_partition=True option and we should determine if t…