Issues

• IndexError in mut_param_dataset_correlation for single-replicate cells

  stub
  matsengrp/multidms#319 · Filter by author jaredgalloway opened on Aug 18, 2026
  

• Write the three missing docs pages (biophysical model, BA.1 fitting example, simulation validation)

  stub
  matsengrp/multidms#318 · Filter by author jaredgalloway opened on Aug 18, 2026
  

• Emit manuscript Figure 2 and SI S1-S5 from the simulation pipeline

  stub
  matsengrp/multidms#316 · Filter by author jaredgalloway opened on Aug 18, 2026
  

• Spike prep diverges from legacy: in-frame codon deletions dropped, replicate subset differs

  stub
  matsengrp/multidms#313 · Filter by author jaredgalloway opened on Aug 18, 2026
  

• mut_type() mislabels in-frame codon deletions as nonsynonymous

  stub
  matsengrp/multidms#312 · Filter by author jaredgalloway opened on Aug 17, 2026
  

• Linear (Identity) baseline arm for the scv2-spike pipeline (SI Figure S10)

  matsengrp/multidms#293 · Filter by author jaredgalloway opened on Aug 5, 2026
  

• Re-express fitted 0.4.0 spike model in PR #164 (main) form; verify Huber loss is preserved (params approximated from ge_fits.png)

  questionwontfix
  matsengrp/multidms#281 · Filter by author Haddox opened on Jul 14, 2026
  

• Concurrent (single-solve) fitting for multidms

  questionwontfix
  matsengrp/multidms#243 · Filter by author jaredgalloway opened on Jun 17, 2026
  

• Add condition-specific mutation names to get_mutations_df

  matsengrp/multidms#192 · Filter by author jaredgalloway opened on Mar 2, 2026
  

• Remove deprecated phenotype_as_effect parameter from get_mutations_df and get_variants_df

  matsengrp/multidms#179 · Filter by author jaredgalloway opened on Dec 3, 2025
  

• citation

  matsengrp/multidms#99 · Filter by author wsdewitt opened on Jul 19, 2023
  3

  

• A ridge penalty that doesn't bias toward WT

  enhancementquestionwontfix
  matsengrp/multidms#51 · Filter by author wsdewitt opened on Mar 2, 2023