search

Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
448 stars 51 forks source link

scipy version adaptation issues #189

Open Zstark11 opened 4 days ago

Zstark11 commented 4 days ago

I need scipy version 1.10.0 when doing VIA trajectory inference. Because if my scipy version is 1.11.4 when I run

v0 = ov.single.pyVIA(adata=adata,adata_key='X_pca',adata_ncomps=80, basis='tsne',
                         clusters='clusters',knn=30,random_seed=4,root_user=[4823],)
v0.run()

will report an error ValueError: mismatching number of index arrays for shape; got 0, expected 2

However, version 1.10.0 of scipy will give an error when performing differential expression analysis of cells when I run dds.deg_analysis(treatment_groups,control_groups,method='ttest') will report an error ImportError: cannot import name 'false_discovery_control' from 'scipy.stats' (/home/zouguoyin/anaconda3/envs/py3.10/lib/python3.10/site-packages/scipy/stats/__init__.py)

Hopefully the scipy version will be unified

DBinary commented 1 day ago

I have the similar bug with you, we will fix this bug quickly. And actually, this bug will not affect the subsequent analyses, the relevant results have been calculated and stored before triggering the bug.

Best wishes, Lei

Zstark11 commented 1 day ago

I have the similar bug with you, we will fix this bug quickly. And actually, this bug will not affect the subsequent analyses, the relevant results have been calculated and stored before triggering the bug.

Best wishes, Lei

Thank you for your efforts