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
Dynamo welcomes contribution (documentation improvement, bug fix, new features / test, organizational improvement, code readability, etc) from the community. The contribution [guidance](https://github.com/aristoteleo/dynamo-release/blob/master/CONTRIBUTING.md) needs to be updated to make this process...
Functions/classes exposed in this modules now have refactored docstrings except the ones in `Markov.py` and some methods of `TRNET` in `sampling.py`. I am now still working on other functions that...
Hi dynamo group, I'm learning dynamo following the tutorial and I'm confused of the result of this code: ``` dyn.pl.jacobian(adata, regulators=['tfec'], effectors=['pnp4a'], basis='umap') # https://dynamo-release.readthedocs.io/en/latest/notebooks/Differential_geometry.html ``` I don't know how...
Hi guys, a quick suggestion: I notice in the sample datasets, the hematopoiesis scNT-seq data can be downloaded either raw or processed, whereas it seems that the only available version...
Can you please explain the function of these option? This option is used in the tutorial (https://dynamo-release.readthedocs.io/en/latest/notebooks/lap_tutorial/lap_tutorial.html) without a clear explanation.
Hi my dear friends, I noticed the umap generated by `dyn.tl.reduceDimension` is not as good as that from other tools (seurat, scanpy, etc.) Here is a umap generated by `dyn.tl.reduceDimension`...
Hello, Thanks for sharing your great work! I would love to use dynamo to analyze some of our data but I'm running into trouble. I have ran dynast (dynast-release 1.0.1)...
Create the template for issues about doc Fix a possible markdown syntax mistake in bug report template
Fix #326 The following APIs are modified to accept `'save'`, `'show'`, '`return'`, `'both'`, and `'all'`: - `pl.cell_cycle_scores` - `pl.connectivity_base` - `pl.nneighbors` - `pl.phase_portraits` - `pl.dynamics` - `pl.fate_bias` - `pl.fate` -...
- Separate Flake8 into its own action, since it doesn't need to be run in a matrix of python versions and is independent of tests - Add `.flake8` config to...
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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