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An issue that has come up for Xenium data is neighbourhood identification. In Visium, it's relatively easy to find neighbours of spots because they are laid out uniformly on the slide. For Xenium, nei…
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In #406 we decided to get rid of `scanpy.api`, which worsened our import time. Thanks to @ivirshup (#703, #704), the main culprits to long import times are out of the game, but there’s still room for …
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如果使用广义模块度进行社区检测的话,会涉及到超参数的选择。大佬有没有了解过这个超参数如何选取的问题,选较少值会生成大的社区,选较大值则会生成小的社区。
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some potential options:
-- Near linear time algorithm to detect community structures in large-scale networks
-- louvain
-- Multi-Threaded Modularity Based Graph Clustering using the Multilevel Paradi…
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Getting the above error when running MoDisco.
Minimal example to reproduce the error:
```
import modisco
import numpy as np
import tensorflow as tf
one_hot = tf.one_hot(np.random.randint(lo…
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Hi
I am having problems loading the localhost page in static mode both on Firefox and Chrome (I am working on a Linux machine and starting local server both in python 2.7 and 3.6 enviroments)
I ca…
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Hi
I would love to be able to try out `Symphony` for label-transfer, but with a set of labels defined by an alternative method to `Harmony`. So for example, starting from an `sce` object where the …
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- [x] Additional function parameters / changed functionality / changed defaults?
- [x] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?
- [ ] New plotti…
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Hello, When I run the T8_Batch.ipynb, I found a problem as following:
`
After flitering: (20139, 11750)
adata = adata[:, adata.var[highly_variable]]: (20139, 3000)
STAGATE_slideseqv2mob_batch…
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**Bug in H5 data assertion for h5ad files**
I tried to use `has_h5_attribute` and `has_h5_keys` to assert scanpy outputs ([here](https://github.com/galaxyproject/tools-iuc/pull/6162#discussion_r173…