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LINDA 0.2.0

New

  • Added constraints_mode to runLINDA() with two values:
    • "hard" uses AS constraints and forces significantly AS-affected reactions to zero.
    • "soft" uses AS-derived reaction penalties in the objective function while keeping reactions feasible.
  • Changed the default splice_effect_sign from "both" to "negative".
  • Restored splice_effect_sign as a user-facing argument in the hard-constrained workflow.

Fixes

  • Fixed documentation inconsistencies around pValThresh, splice_effect_sign, and the hard/soft AS modes.
  • Fixed AS score integration when as.input = NULL in the soft workflow.
  • Made AS input handling robust to extra columns by explicitly selecting id, effect, and significance.
  • Allowed top = "all" in input validation, matching existing bin_measurements() behavior.
  • Improved validation messages for solverPath, threads, and save_res.