dynamo-release

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Remove `highest_frac_genes` by `cleanup()` before saving and remove long nxviz warning

1

Issue arised in the newest release version, related to anndata's saving issue regarding pandas.Series Fix verified:

dummyindex

TypeError: Image data of dtype object cannot be converted to float for Response heatmap

4

Hello Dynamo, I was running the `Cell-wise analyses` tutorial. It was smooth until the Response heatmap. I got a `TypeError: Image data of dtype object cannot be converted to float`....

hyjforesight

Hello Dynamo, When setting the initial cells and target cells for LAP, the fixed points which represent the cell state should be defined. I chose the fixed points 13, 6,...

hyjforesight

Is there a detailed tutorial of Lineage tree of hematopoiesis?

1

Hello Dynamo, I'm wondering whether we have a detailed tutorial for plotting lineage tree of hematopoiesis (https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_megakaryocytes_appearance/tutorial_hsc_dynamo_megakaryocytes_appearance.html). Thanks! Best, YJ I did like this. ```python dyn.pd.tree_model(adata, group='cell_type', progenitor='HSC', terminators=["Meg", "Ery",...

hyjforesight

Issue of import dynamo

6

Hi dear professor, After finishing install of dynamo on my MAC book, I failed to import dynamo at the first step, could you help me solve the problem, thank you...

wulc21

KeyError with running dynamics

3

Hello, I am very new to using this package and I am unable to run the dynamics function on my data because of a KeyError. I am not sure how...

michelle-mantilla

GATA2-PLEK pair cannot be found in 'Minimal network for basophil lineage commitment' tutorial

6

Hello Dynamo, When I was running this tutorial (https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_basophil_lineage/tutorial_hsc_dynamo_basophil_lineage.html), only 4 rows of switch gene-pairs were found. There is no GATA2-PLEK pair like the tutorial said. Do I miss something?...

hyjforesight

matplotlib 3.5.1 compatibiliy known issue collection

5

Our notebooks are tested generally on matplotlib **3.4.3**. Know issues with matplotlib 3.5.1: - tight_layout() - animation #318 #297

dummyindex

as stated above, let us make sure vecfld / VectorField2D used consistently in all topography plots

Xiaojieqiu

 Installation method `pip install dynamo-release` Environment A new environment created via conda -n newEnv python=3.8 Python version 3.8 Solution should be fixed in dev ver.

dummyindex