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Hi,
We want to use monocle3 for pseudotime analyze. But it generate a totally different UMAP than Seurat and it split into too many clusters. Monocle3 generates pseudotime based on UMAP. Can we us…
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Communities in a graph could be calculated (e.g. Louvain modularity) and clustering/grouping (alternative to existing Markov clustering) could be done based on that. Let's investigate whether anything…
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- [x] I have checked that this issue has not already been reported.
- [x] I have confirmed this bug exists on the latest version of scanpy.
- [ ] (optional) I have confirmed this bug exists on the m…
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When trying to follow the [tutorial](https://nbviewer.jupyter.org/github/colomemaria/epiScanpy/blob/master/docs/tutorials/ATAC_bld_ct_mtx_tutorial.html) on creating scATAC-seq count matrices from [bam…
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Ingest tries to search for the metric used when neighbors was called. When this information is not available it fails. Is there a workaround for this?
```python
adata = sc.datasets.pbmc68k_…
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Hi,
I would like to get some advice on selecting the appropriate clustering method for the Slingshot analysis. My goal is to infer the trajectory of progression (and potentially bifurcations) from …
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I just ran a test job for this App and it failed with the following error message.
```
+ chmod +x main.py
+ SINGULARITYENV_PYTHONNOUSERSITE=true
+ singularity exec -e docker://filsilva/cxnetwork…
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Hello,
I'm trying several graph based clustering methods for single cell rna-seq data including seurat, monocle and scanpy. I'm trying to understand how the clustering function works in each of th…
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Hi, first of all thanks for your great job!
I'm new on this kind of analysis so I have a few doubts interpreting the results, I hope this doesn't bother you too much.
I was testing a pipeline with …
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https://mp.weixin.qq.com/s/MsU7WaqvLFA9Y-wetT_pfA
ixxmu updated
3 years ago