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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Problems with importing for new, Tutorial: Perturbation simulation #467

Open finncreeggan opened 2 months ago

finncreeggan commented 2 months ago

Describe the bug I am having a problem importing a module 'scenicplus.dimensionality_reduction'. I am running the basic Perturbation simulation tutorial with the most recent version of scenicplus.

To Reproduce from scenicplus.simulation import ( train_gene_expression_models, simulate_perturbation, plot_perturbation_effect_in_embedding )

Error output

ModuleNotFoundError Traceback (most recent call last) Cell In[6], line 1 ----> 1 from scenicplus.simulation import ( 2 train_gene_expression_models, 3 simulate_perturbation, 4 plot_perturbation_effect_in_embedding 5 )

File ~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/simulation.py:12 9 from scipy.stats import norm as normal 11 from .eregulon_enrichment import score_eRegulons ---> 12 from .dimensionality_reduction import plot_metadata_given_ax 13 import matplotlib.pyplot as plt 14 import logging

ModuleNotFoundError: No module named 'scenicplus.dimensionality_reduction'

Expected behavior i expected all the modules to be loaded andbe in scenicplus

screenshot Screenshot 2024-09-12 191252

Version:

SeppeDeWinter commented 1 month ago

Hi @finncreeggan

Are you sure that you installed the newest version of SCENIC+ from GitHub? The code that produces the error you are showing does not exist anymore in the main branch of SCENIC+.

Please pull the newest code and try to reinstall.

All the best,

Seppe