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I was wondering if there is a way to plot dots in the order of expression, similar to sort_order parameter in scanpy `sc.pl.umap` (https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.umap.html…
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Hi,
I have been trying to run talon filter on my database:
```talon_filter_transcripts --db talon/database.db -a Hg38 --maxFracA 0.5 --minCount 1 --minDatasets 3 --o talon/talon_run.csv```
An…
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### What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
### Please describe your wishes
10X updated to Space Ranger v3.0, and …
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### What kind of feature would you like to request?
Other?
### Please describe your wishes
Another point that I'd like to throw into the scanpy 2.0 discussion:
Right now, many functions h…
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Scanpy can't run on Pulsar due to it collecting it's outputs via wildcards.
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how to solve TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices'
TypeError Traceback (most recent call last)
Cell In[70]…
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Some issues I found in the current implementation:
1. Some implementation omits customized preprocess steps: **DeepST**. did @shdam find anything from the methods you worked on?
2. Some impleme…
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Hi, this is really a practical tool! I was wondering if python users(scanpy users) could benefit from this, particularlly when Seurat can not handle million-scale cells caused by a known issue, i.e., …
SNOL2 updated
4 months ago
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I was originally trying to use the `rank_genes_groups()` function in scanpy to get p-values and logfoldchanges between a single condition and a reference condition. My end-goal was to take the DE res…
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- [x] Additional function parameters / changed functionality / changed defaults?
Hi ScanPy team
I emailed @ivirshup but others should be involved I think.
This function would be usef…