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cNMF_perturbed_gene_analysis.py crashes when mdata['rna'].X contains raw counts

Status: Open.

#9 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026

merge_pdfs_in_folder hangs indefinitely with PyPDF2 PdfMerger on thousands of PDFs

Status: Open.

#8 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026

cNMF_program_analysis.py pre-loop correlation step balloons memory past 700 GB on moderately-sized datasets

Status: Open.

#7 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026

programs_dotplots looks for h5mu at <run>/adata/ but Stage 1 inference writes to <run>/Inference/adata/

Status: Open.

#6 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026

compute_fake_perturbation_tests crashes with AttributeError: 'Namespace' object has no attribute 'reference_targets'

Status: Open.

#2 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026

compute_fake_perturbation_tests memory grows ~15 GB per iteration -> OOM at iter ~16/50 on real datasets

Status: Open.

#3 In EngreitzLab/PerturbNMF;

· adamklie opened on May 10, 2026