dynamo-release
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aristoteleo
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
As part of our ongoing effort to enhance the quality and reliability of our project, we should improve our test files to make them well-structured and comprehensive. - [x] Remove...
It seems that if we initialize the value in a dictionary `adata.uns[key]` with None, it will be ignored when saving to h5ad. As a result, when we load the file,...
- [x] I am sure this issue is not simply a general python programming problem (if so, please google the answers). - [x] I have searched github issues and confirm...
It will be nice to integrate an AI assistant like [this one](https://docsgpt.arc53.com).
Hi, I intend to use umap or other dimension reduction tools to compute the in-silico perturbation. My code is: ``` dyn.vf.VectorField(adata, basis='umap') gene = "Gata1" dyn.pd.perturbation(adata, gene, [-100], emb_basis="umap") dyn.pl.streamline_plot(adata,...
when using datashader to plot the umap or other embeddings, the current implementation fails. There are a few specific bugs: when using despline, the ax in datashader is an `Image`...
Refactor and optimize the functions in `dynamo.tl`. Including: - [x] Resolve the TODO list in graph_calculus.py - [ ] Refactor dynamics. - [x] Debug and optimize the reduceDimension function, and...
I would like to use the function `f(x)` like you describe it in the "10min to dynamo" tutorial [1] to get the velocity for unseen gene expression vectors `x`. Unfortunately,...
This PR currently just adds two tests, one were running `tl.cell_velocities` works and one were selecting for `transition_genes` fails. From trying to debug it, I would say that there is...
Workaround for issue https://github.com/aristoteleo/dynamo-release/issues/561 (or issue https://github.com/aristoteleo/dynamo-release/issues/440), where anndata dictionary entries with None values are deleted when `adata.write()` is called.
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Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses