dynamo-release

dynamo-release copied to clipboard

`dyn.pl.scatters` legends crowd together in the last figure when "ax" specified and show_legend='on data'

2

- [x] I am sure this issue is not simply a general python programming problem (if so, please google the answers). - [x] I have searched github issues and confirm...

chansigit

Unable to download sample data

2

Hi, dynamo group I'm learning dynamo following the tutorial, but sometimes it's hard to download sample data especially when I stay at home. ``` >>> adata = dyn.sample_data.zebrafish() |-----> Downloading...

FionaMoon

IndexError: list index out of range

4

dyn.tl.cell_velocities(adata) --------------------------------------------------------------------------- IndexError Traceback (most recent call last) /tmp/ipykernel_21547/875872558.py in ----> 1 dyn.tl.cell_velocities(adata) /opt/conda/envs/dynamo/lib/python3.7/site-packages/dynamo/tools/cell_velocities.py in cell_velocities(adata, ekey, vkey, X, V, X_embedding, transition_matrix, use_mnn, n_pca_components, transition_genes, min_r2, min_alpha, min_gamma, min_delta, basis,...

Jeffyang123

dynamo downloads wrong datasets for scNT_seq

1

Hi, very quick issue: I have dynamo version 1.1.0, and if I run either `dyn.sample_data.scNT_seq_neuron_labeling()` or `dyn.sample_data.scNT_seq_neuron_splicing()` it seems to download the zebrafish dataset instead. Maybe the files have been...

rorymaizels

Hi, thanks for your previous help. I have used my own dataset to run several times, and its results are different from the picture. Do you have any better suggestions?...

ergezhenshuai

update velocity class to enable cell-wise beta/gamma input

3

- [ ] currently dynamo can use cell-wise alpha to calculate RNA velocity but it doesn't support cell-wise beta and gamma, support this

Xiaojieqiu

correctly use total RNA or splicing RNA gamma

3

- [ ] dynamo currently doesn't distinguish total RNA or spliced RNA based gamma, we need to make sure we are using the correct gamma

Xiaojieqiu

add an article to summarize the method we developed for estimating kinetic parameters for the labeling data

3

- [ ] add an article to summarize the method we developed for estimating kinetic parameters for the labeling data - [ ] we may also do this for the...

Xiaojieqiu

Add `calc_new_to_total_ratio()` in __init__

1

Sichao25

Missing LinearODE methods in mix_kin_deg and mix_pulse_chase experiments.

2

- [x] I am sure this issue is not simply a general python programming problem (if so, please google the answers). - [x] I have searched github issues and confirm...

Sichao25