Skip to content

analysis_and_comparison.md

Latest commit

 

History

History
22 lines (17 loc) · 1.08 KB

analysis_and_comparison.md

File metadata and controls

22 lines (17 loc) · 1.08 KB

Analysis & comparison

Analyses — {mod}raven_toolbox.analysis

RAVEN analyses that are not in cobrapy's core:

  • {func}raven_toolbox.analysis.reporter_metabolites — Reporter Metabolites, an around-metabolite gene-score test. raven-toolbox uses an exact closed-form background in place of RAVEN's Monte-Carlo.
  • {func}raven_toolbox.analysis.fseof — Flux Scanning based on Enforced Objective Flux: regression slope + correlation, with amplify / knockdown / knockout classes and gene aggregation.
  • {func}raven_toolbox.analysis.random_sampling — random-objective flux sampling (wraps cobra's samplers); {func}raven_toolbox.analysis.find_good_reactions is the companion screen.

Comparison — {mod}raven_toolbox.comparison

{func}raven_toolbox.comparison.compare_models compares any number of models and returns tidy DataFrames (reaction / metabolite / gene / subsystem presence, pairwise Jaccard, and an optional check_tasks pass/fail matrix). Plotting and tSNE/MDS are deliberately left out — they are one-liners in seaborn / scikit-learn on the returned frames.