aristoteleo dynamo-release issues

aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

https://dynamo-release.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

420 stars 59 forks source link

issues

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Optimize the display of the tutorial page and add `adjust_legend` argument

#707 Starlitnightly opened 1 month ago
4
Updated of dynamo 1.4.2

#706 Starlitnightly opened 1 month ago
0
Perturbation will not run when only using n_cells for Jacobian calculation

#705 styounes opened 1 month ago
3
Update README.md

#704 YanshiHu closed 3 weeks ago
2
How can I obtain the synthesis rates for each gene in each cell?

#703 Rcheng0731 closed 2 months ago
0
Bump jupyterlab from 3.6.7 to 3.6.8

#702 dependabot[bot] opened 2 months ago
0
Bump version: 1.4.0 → 1.4.1

#701 Sichao25 closed 2 months ago
1
Debug duplicate signatures in `numba.vectorize()`

#700 Sichao25 closed 3 weeks ago
1
can't get dyn.tl.moments to work

#699 paupaiz opened 3 months ago
2
Debug set_figure_params

#698 Sichao25 closed 3 months ago
1
Debug: shape and name mismatch in cell-wise alpha saving

#697 Sichao25 closed 3 months ago
1
Debug: The sizes of the scatter plots are not set correctly.

#696 Sichao25 closed 3 months ago
1
Deprecate more sparse matrix .A attributes

#695 Sichao25 closed 4 months ago
0
Can't get dyn.tl.dynamics(adata) to work

#694 wodigraf opened 4 months ago
2
Include `igraph` leiden implementation

#693 Sichao25 opened 4 months ago
1
Replace `louvain` with `leiden`

#692 Sichao25 closed 4 months ago
0
Deprecate `.A` attributes of sparse matrix in Sijie july24 fix

#691 Sichao25 closed 4 months ago
0
init a branch for fixing

#690 chansigit closed 4 months ago
0
Failed building wheel for louvain when I tried to install dynamo-release

#689 ruifengy closed 2 weeks ago
7
Dropbox link in ERCC relative2abs is no longer available.

#688 chansigit closed 2 weeks ago
1
defects in `get_data` failed the sample data and blocked the unit test cases

#687 chansigit closed 3 months ago
1
Fix matplotlib version issues and a circular import issue

#686 chansigit closed 4 months ago
6
Migrate to Numpy 2.0.0

#685 Sichao25 opened 5 months ago
1
Upgrade code coverage to v4

#684 Sichao25 closed 4 months ago
1
Debug `pl.circosPlot()`

#682 Sichao25 closed 3 weeks ago
1
Debug `pl.highest_frac_genes()`

#681 Sichao25 closed 4 months ago
1
gene names missing when using dyn.pl.highest_frac_genes

#680 chansigit closed 3 months ago
2
Constraint on matplotlib version

#679 Sichao25 closed 5 months ago
0
Input X contains NaN.

#678 christophechu opened 6 months ago
5
Debug test_gradop

#677 Sichao25 closed 6 months ago
0
LinAlgError when running dyn.tl.dynamics()

#676 nprashant2001 opened 6 months ago
8
Separate two condition and fix the grid

#675 feanaros closed 1 month ago
21
Optimize chunked preprocessing

#674 Sichao25 opened 7 months ago
1
Most probably path predictions: error message: 'networkx.convert_matrix' has no attribute 'from_scipy_sparse_matrix'

#673 fengshuoliu closed 8 months ago
2
Which two layers of dynast are suitable as new and total for scNT-seq？

#672 mingjianPeng closed 4 months ago
2
Add `calc_new_to_total_ratio()` in __init__

#671 Sichao25 closed 3 weeks ago
1
Error about group parameter in dyn. tl. dynamics

#670 mingjianPeng closed 1 month ago
6
Update matplotlib `Colorbar.draw_all()` to `Colorbar._draw_all()`

#669 Sichao25 closed 8 months ago
1
Missing return value in `.pl.lap_min_time()`

#668 Sichao25 closed 8 months ago
0
Docstring and type hints for root folder python files

#667 Sichao25 closed 8 months ago
1
Docstring and type hints for the prediction module

#666 Sichao25 closed 8 months ago
1
Extra filter after pearson residuals normalization

#665 Sichao25 closed 8 months ago
1
Debug the preprocessing of integer matrix input

#664 Sichao25 closed 8 months ago
1
Add missing return value to deprecated functions

#663 Sichao25 closed 8 months ago
1
Reorganize estimation module

#662 Sichao25 closed 8 months ago
1
Update docstr and type hints for External module

#661 Sichao25 closed 8 months ago
1
Add doctring and type hints for simulation module

#660 Sichao25 closed 8 months ago
0
Is there a function that can generate velocity graph, similar to scv.tl.velocity_graph?

#659 VivLon closed 9 months ago
2
Debug simulation module

#658 Sichao25 closed 9 months ago
1
Debug networks plot

#657 Sichao25 closed 8 months ago
0