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Currently, `sc.tl.louvain` etc return cluster assignments as a Categorical with dtype `str` resulting in incompatibility with matplotlib color sequences. For example, the following code raises a Value…
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I have two suggestions/questions about dot/matrix plots:
1- If `standard_scale='var'` is given, we can write `Mean expression\nin group\n(min-max scaled)` on the color legend to be more accurate ab…
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Thank you for developing the excellent tool Pegasus. I am a beginner in single-cell genomics analysis and started with Seurat in R, later learned Scanpy in Python, but I find Pegasus more suitable for…
x1han updated
1 month ago
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Hi, I tried to using `stereopy` to analysis my `stereo-seq` samples. I create a `ms_data` object from 3 slices according to the [tutorial](https://stereopy.readthedocs.io/en/latest/Tutorials%28Multi-s…
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I've been trying to follow the example in order to reconstruct MSMT on my own data and fit method resulted in NaN values. So I used the example itself, step by step, and it turned out to return NaN va…
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Hi there, not sure whether this is really a bug, but if I make certain changes to a `MuData.obs` (e.g. removing duplicate columns), the `obs` in the copy becomes different from the original.
**Ex…
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Hi, I am a new of Rust. Now I am trying to implement the "arrange.rs" which is the first example in the examples of differential dataflow. when I try to run cargo build,I think this step is just to do…
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For the batch integration embedding task we have developed this package:
https://scib-metrics.readthedocs.io/en/stable/
with python-only, jax-based implementations. This would easily allow fast …
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His next claim is that it is very unlikely that there would be bats naturally living in the metropolitan distict of Wuhan, and in fact no bats were traded at the market at all.
Let us go one step f…
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Hi,
I am running pySCENIC following this vignette:
https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Integration%20with%20scanpy.ipynb
Everything runs smoothly until the…