Refactor InferelatorJL + add evaluation pipeline#1
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sheyiphunmi wants to merge 14 commits intomainfrom
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Refactor InferelatorJL + add evaluation pipeline#1sheyiphunmi wants to merge 14 commits intomainfrom
sheyiphunmi wants to merge 14 commits intomainfrom
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…N2 → refineTFA for clarity
…N2 → refineTFA for clarity
…tep 7 evaluation to examples - Add applyTimeLag/applyTimeLag! with timeLagFile/timeLag params wired through refineTFA, inferGRN, and run_pipeline functions - Fix evaluateNetwork to wrap computePR instead of computeMacroMetrics - Fix matplotlib heightRatios → height_ratios in PlotBatch.jl - Fix edgeSS > 0 code path (rand → StatsBase.sample, median → dropdims) - Replace println with @info/@warn throughout src/ - Add Step 7 evaluation section to all four example scripts - Add applyTimeLag test set to runtests.jl
Update README and add instability diagnostic plots - Update README: add step 3b/7 to pipeline, fix output filenames, add timeLagFile/timeLag params, fix evaluateNetwork signature, add dev example files to examples table - Add plotInstabilityCurves (src/grn/PlotInstability.jl): auto-generated network-level λ selection diagnostics; standalone per-gene mode - Add lambdaRangeWarm and targGenes to GrnData for plot support
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Summary
Major refactor of InferelatorJL repository.
Changes
Notes
This is a large architectural update (dev-refactor branch).
Please review carefully before merging.