dynamo-release

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Animatation _ attribute error

1

  Dear Qiu： Im running the tutorial “Conventional SCRNA-seq: Zebrafish pigmentation”. and run into a attribute error in the section of **Animatation**. thanks in advance

lgmp315

scNT-seq data not found

6

Hello Qiu, Thank you for all the information provided and the very detailed tutorials. I went through the zebrafish tutorial and now I would like to compare the estimated lineages...

mkyriak

support setting a resolution for vectorfield clustering

1

Changes: 1. add **kwargs for the leiden(), louvain(), infomap() function calls in dyn.vf.cluster_field(), otherwise the function can only use default resolution settings 2. add a `resolution` parameter explicitly so users...

chansigit

acceleration/curvature layer missing when using umap

1

it seems that the current implementation of curvature() and acceleration() only insert a new layer when `basis=pca` I calculated the acceleration using umap and ran the rank test ``` dyn.vf.acceleration(adata,...

chansigit

Can I specify ident_1, ident_2 for rank gene analysis methods like Seurat?

1

Dear developers, In Seurat's differentially expressed gene analysis function FindMakers(), there are "ident.1" "ident.2" parameters specifying group 1 vs group2. With these settings, users could flexibly compare customized two groups'...

chansigit

Does the group parameter of tl.dynamics() correspond to the "Differential Kinetics" in scvelo?

1

The document says that by specifying 'group' it enable estimating group-specific kinetics parameters. Is it an implementation similar to the scvelo "Differential Kinetics" (https://scvelo.readthedocs.io/DifferentialKinetics/)? If yes, should I run similar...

chansigit

Problem of LAP

3

Hi, I try to run the LAP's tutorial, and I get a different result of kinetic_heatmap( HSC->Bas) as the fig1. GATA2 was expressed from high to low in my result,...

mhtksc

Failure to generate vectorField: 'numpy.ndarray' object has no attribute 'setdiag'

5

Hi all, I am having an issue with the dyn.vf.VectorField(adata_dyn_cc, basis='umap', M=1000, pot_curl_div=True) function. I get the following error when I set pot_curl_div=True, but I can generate a vector field...

arnav-mehta

We would like to enable 3D quiver and scatter plot in dynamo. To start with, we will matplotlib for those implementations but may consider implementing via PyVista in the future....

Xiaojieqiu

[old released version on Pypi] Dependencies issue. Newer pandas version yields a KeyError with dyn.pp.recipe_monocle

4

Hi! Thanks for developing and maintaining Dynamo, congratulations for your great work. I am trying to play around with the Dentate Gyrus example and I got an error that has...

LidiaML