scanpy
pagoda2
| scanpy | pagoda2 | |
|---|---|---|
| 5 | 2 | |
| 1,757 | 191 | |
| 1.7% | 2.1% | |
| 9.3 | 5.3 | |
| 6 days ago | 2 months ago | |
| Python | JavaScript | |
| BSD 3-clause "New" or "Revised" License | - |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
scanpy
- Renaming Genes for Scanpy Plot
- Useful Python Decorators for Data Scientists
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[Scanpy] Installation issues related to pytables
Upon searching stack, I still do not understand the exact issue, as the file "hdf5extension.cp38-win_amd64" is present within C:\Users\username\anaconda3\lib\site-packages\tables\. Would anyone be able to explain the problem and any potential circumventions?
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standardize/normalize seq data
I would suggest you explore with SCANPY and verify if your batch labels generate a strong separation in your samples (PCA, tSNE, UMAP). If you then need to correct for batches, according to how simple/complex they are, you can choose a tool from this benchmark.
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Flipping one histogram below the axis.
I am plotting 2 1-D histograms on top of one another using a hold on command. Is there a way to have one histogram be upside down, and then to flip the entire plot 90˚? I am looking to create a violin plot https://github.com/theislab/scanpy/issues/1448 on my own, having one histogram on the left, and one on the right.
pagoda2
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GOterm analysis in Seurat
Try pagoda2 for this: https://github.com/kharchenkolab/pagoda2
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Seurat Vs Pagoda2 For Scrnaseq Analysis
I realize that this is a bit old, but I find pagoda2 faster: https://github.com/kharchenkolab/pagoda2
What are some alternatives?
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