dynamo-release

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Question about rank acceleration

5

Hi, I have a simple questions about rank acceleration. Is `abs` just changing the sign? If yes, Why is `BIK` ahead of `S100A6` in column 1 of `rank_abs_acceleration` as follows:...

lh12565

Correct spliced RNA velocity

13

Hi, my data was obtained the conventional scRNA-seq technique (10X) with no labeling data. I found the nonsensical velocity flow from macrophage to monocyte using dynamo. I found your article...

lh12565

AttributeError: 'AnchoredSizeLocator' object has no attribute 'get_subplotspec'

8

Hi, I installed dynamo with python 3.10.2 using pip install dynamo-release I then downloaded your zebrafish tutorial https://raw.githubusercontent.com/aristoteleo/dynamo-tutorials/master/zebrafish.ipynb and tried to run it (see pdf attached): [zebrafish.pdf](https://github.com/aristoteleo/dynamo-release/files/8054077/zebrafish.pdf) I got an...

DanieleMuraro

There is an import issue mentioned in GiulioRossetti/cdlib#201, which may cause problems for users with specific OS. This issue is related `cdlib`'s `infomap` package import. expected fixes: 1) provide better...

dummyindex

ddhodge refactor: assume adj_mat is sparse matrix and adjust related code snippets

1

dummyindex

About data in scNT-seq

4

Dear Dr Qiu, Thank you very much for this great package. I found you use tow data sets in scNT-seq. One is splicing dataset. Another is labeling dataset. Splicing dataset...

houruiyan

add an utility function to identify bad genes with ntr goes up for a degradation experiment

1

If the ntr goes up for a gene in a degradation experiment, this may indicates some technical issues because the RNA should always decay for a chase experiment. Add a...

Xiaojieqiu

Harmonize anndata layer nomenclature in a pulse - chase experiment

1

Hi Xiaojie, Currently the input to dyn.tl.recipe_deg_data requires the layer with labeled counts to be named 'new'. To better reflect the nature of those counts in a pulse chase experiment,...

jmartinrufino

We need to update our contributing guidelines so that they can guide other developers.

Xiaojieqiu

There are a lot of frequently asked questions (FAQs) regarding dynamo from the community. We should add a FAQ page in our docs for the benefits of our great community!

Xiaojieqiu