Wang Jinzhang
Wang Jinzhang
**Describe the bug** **To Reproduce** imputed_acc_obj = impute_accessibility( cistopic_obj, selected_cells=None, selected_regions=None, scale_factor=10**6 ) **Error output** --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[66], line 3 1 from typing import...
**Describe the bug** A clear and concise description of what the bug is. **To Reproduce** plot_metadata( cistopic_obj, reduction_name='UMAP', variables=['log10_unique_fragments_count', 'tss_enrichment', 'Doublet_scores_fragments', 'fraction_of_fragments_in_peaks'], target='cell', num_columns=4, text_size=10, dot_size=5) **Error output** File ~/anaconda3/Git/pycisTopic/src/pycisTopic/clust_vis.py:571,...
**Describe the bug** CalledProcessError: Command '['/home/taxue/mywork/pycisTopic/Mallet-202108/bin/mallet', 'import-file', '--preserve-case', '--keep-sequence', '--token-regex', '\\S+', '--input', './scratch/leuven/330/vsc33053/ray_spill/mallet/tutorial/corpus.txt', '--output', './scratch/leuven/330/vsc33053/ray_spill/mallet/tutorial/corpus.mallet']' returned non-zero exit status 127. **To Reproduce** os.environ['MALLET_MEMORY'] = '200G' from pycisTopic.lda_models import run_cgs_models_mallet #...
Hello, I have a bit of confusion about the Direct and Extended Predicted TF-to-region-to-gene links. I do not understand why there is a distinction between Direct and Extended, what is...
Hello, dear Sevan, After running the scenicplus pipeline, I obtained ctx_results.hdf5 AND dem_results.hdf5 result where I generated 25 topics and annotated eight cell types in my work. However, the results...