Refactor InferelatorJL + add evaluation pipeline#1

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sheyiphunmi wants to merge 7 commits intomainfrom

Commits on Mar 29, 2026

Initial commit: refactored Inferelator codebase
Seyifunmi Owoeye
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Add evaluation pipeline (R-based GRN benchmarking tools)
Seyifunmi Owoeye
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Merge remote-tracking branch 'origin/main' into dev-refactor
Seyifunmi Owoeye
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Refactor GRN module: rename combineGRN → aggregateNetworks, combineGRN2 → refineTFA for clarity
Seyifunmi Owoeye
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Refactor GRN module: rename combineGRN → aggregateNetworks, combineGRN2 → refineTFA for clarity
sheyiphunmi
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Commits on Mar 30, 2026

Bringing codebase closer to publication
sheyiphunmi
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Commits on Mar 31, 2026

Updated gitignore file
sheyiphunmi
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