cellDancer

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error of cd.pseudo_time()

2

**I run cd.pseudo_time() same as that in the Case study 1:** import random dt = 0.05 t_total = {dt:int(10/dt)} n_repeats = 10 cellDancer_df_update = cd.pseudo_time(cellDancer_df=cellDancer_df, grid=(30,30), dt=dt, t_total=t_total[dt], n_repeats=n_repeats, speed_up=(100,100),...

datou99

torch version compatibility

1

It seems that cellDancer relies on torch version = 1.10.0. However, my current torch version is 2.0.0. I tried to install 1.10.0 but it seems that it is no longer...

stemjn

Best Practice for Analyzing Multiple Single-cell Sequencing Samples with CellDancer

1

Hello CellDancer Developers, I'm working with multiple single-cell sequencing samples and am seeking advice on the best approach to analyze RNA velocity using CellDancer. Should I merge the samples and...

weir12

The plot of RNA velocity has no arrows

5

`Hi,` I'm having another problem when plotting RNA velocity. The following is my command: ``` cellDancer_df=cd.compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gene', expression_scale='power10', projection_neighbor_size=5, speed_up=(100,100)) fig, ax = plt.subplots(figsize=(10,10)) cdplt.scatter_cell(ax, cellDancer_df, colors=color_dict, alpha=0.5, s=30, velocity=True,...

zcaiwei

cellDancer does not use GPU

1

Hi! I just saw that cellDancer is not using the GPU on my system (by running the nvidia-smi command). Is that expected? If not is there anything I can try...

AlexanderAivazidis

Cannot install the package

2

 

aqlkzf

How to select gene list

1

Hi Doc ex： gene_list=['Smarca2', 'Rbms2', 'Myo1b', 'Hba-x', 'Yipf5', 'Skap1', 'Smim1', 'Nfkb1', 'Sulf2', 'Blvrb', 'Hbb-y', 'Coro2b', 'Yipf5', 'Phc2', 'Mllt3'] loss_df, cellDancer_df=cd.velocity(cell_type_u_s,\ gene_list=gene_list,\ permutation_ratio=0.125,\ n_jobs=8) I don't know how to selsect gene_list...

mabaoweireadingene

Do we have a function to compute RNA velocity for cell by gene matrix?

1

Hi, I wonder if there is any function in celldancer which can generate the raw RNA velocity matrix. I intend to compare this method with other RNA velocity estimation method....

HelloWorldLTY

pseudo_time() error: MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS

1

Hi, I'm getting an error during `peudo_time()`: ``` File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) File "/cluster/work/moor/.snakemake/conda/bf69db601187e32c2ff18c90452fc61d_/lib/python3.7/site-packages/celldancer/pseudo_time.py", line 419, in recur_cell_time_assignment_intracluster MAX_ALLOWED_TERM_CELLS=MAX_ALLOWED_TERM_CELLS) [Previous...

Thapeachydude

The velocity1 and velocity2 values in celldancer_df are NaN

1

Hi, When I'm running the command `cellDancer_df=compute_cell_velocity(cellDancer_df=cellDancer_df, projection_neighbor_choice='gene', expression_scale='power10', projection_neighbor_size=10, speed_up=(100,100))` , I'm having the following problem：  Can you tell me how to tune the parameter to avoid generating...

zcaiwei