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- download a data of choice from 10x genomics with `sc.datasets_visium_sge()` (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- run the scanpy tutorial,…
giovp updated
3 years ago
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I encountered a strange situation, after the integration of batches., the cNMF result file cNMF.usages.k_28.dt_2_0.consensus.txt is blank. Other result files, such as cNMF.gene_spectra_score.k_28.dt_2…
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## Description
See if we can lazily-load `napari/pyqt5`, think these should be the main culprits (need to verify).
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Hi, the [introduction slides with the video transcripts](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna-intro/slides.html) were based on the [slide deck fr…
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I agree with @adrianveres [here](https://twitter.com/adrian_veres_/status/1105969701094674432?s=11): GLM-PCA by @willtownes seems like a rigorous way to deal with zero inflation, since we use PCA as b…
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We've started implementation of a Multimeasure class, which holds multiple AnnData objects (https://github.com/theislab/anndata). These AnnData objects are the primary object used by scanpy (https://g…
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### Please make sure these conditions are met
- [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.
- [ ] (option…
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- [x] New plotting function: A kind of plot you would like to seein `sc.pl`?
- [x] External tools: Do you know an existing package that should go into `sc.external.*`?
Hi, thanks for developing su…
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I tried running the RAPIDS implementation of rank_genes_groups alongside the Scanpy CPU implementation on the same data matrix, but I'm getting very different results.
Here's my code for the GPU ca…
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### Please make sure these conditions are met
- [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.
- [ ] (op…