scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- read_10x_mtx with different prefixes for the barcodes, features and matrix files
- Scanpy neighbors bug with identical/almost identical cells.
- Add support for passing boolean columns in .obs when plotting clustermap or dendrogram.
- Document parameter "dot_color_df" for Dotplot
- Scanpy.pl.embedding throws error when projection='3d' and all values are the same for coloring
- Implement SWNE embedding
- "batch_size" parameter doesn't work for "sc.external.pp.scanorama_integrate"
- Add `scanorama.correct_scanpy` function to `sc.external.pp`
- tsne vs umap with square root/pearson residue normalization
- `sc.pl.heatmap` (and others) should offer a means of accessing the `matplotlib.pyplot.Figure` object
- Docs
- Python not yet supported