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I want to start off by mentioning how much I love scanpy. I recommend this package to everyone I know who is doing single cell sequencing. I love how PAGA and UMAP can be integrated together. PAGA mak…
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Hi!
Thank you so much for publishing the pipeline but I am having some errors getting the pipeline working properly.
Starting with the igraph version error, adding in louvain and cairocffi as …
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Hi,
Thanks again for the great work. :)
I'm testing cellrouter with our own data (Two conditions at day 3). There are ~20 cell sub-populations identified. K = 12 which was defined by findK functio…
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[As described here](https://www.dama.upc.edu/en/publications/fp546prat.pdf) The algorithm claims to be more scalable than `multilevel.community` and to yeild better results on large graphs.
[There's…
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Hi,
I was interested in getting your tutorial to work, but ran into some issues. When I ran the code on you github repo:
```python
import numpy as np
import scanpy as sc
import scdemon as sm
…
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Trying to run the Rphenograph function; it seems to remove one entry.
Run Rphenograph starts:
-Input data of 366047 rows and 8 columns
-k is set to 10
But the output matrix has 366046 rows…
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Dear team,
It is hard to install tkna in a conda environment, the infomap was cannot complie without any instruction like gcc version in infomap github page.
Anyway, I'm using your interface …
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Dear all,
When generating graph genome according to the pipeline https://github.com/pangenome/HPRCy1, I found that some long assembled contigs (generated using hifisam) can not be aligned to the re…
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Hi there,
Thanks for the package.
When I was running `FindClusters(algorithm=4)`, I encountered this Warning. Should I be worried about it? If so, would you mind helping me diagnose this warni…
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To generate the plot after the TSNE you are proposing this code:
![image](https://github.com/xuxiaohan/MSNE/assets/74925521/97b0c7a7-a873-4664-987b-b1f8d2275b5b)
But i am not sure what is the vari…