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Feature/omics layers#49

Merged
DanielGarbozo merged 5 commits into
BigMindLab:devfrom
DanielGarbozo:feature/omics-layers
May 19, 2026
Merged

Feature/omics layers#49
DanielGarbozo merged 5 commits into
BigMindLab:devfrom
DanielGarbozo:feature/omics-layers

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Summary

This PR introduces a new omics-layers feature set to OmicsKit, adding survival analysis utilities,
multi-omics visualization functions, and genomic track support, along with full documentation and tests
for each addition.

New Functions

  • get_cox() + nice_forest() – Cox proportional hazards regression and forest plot visualization for survival analysis.
  • get_glm() + nice_ROC() – Generalized linear model fitting with ROC curve visualization for binary outcome analysis.
  • trend_filter() / updated detect_filter() – Trend-based filtering utilities for omics feature selection.
  • nice_KM() – Kaplan-Meier survival curve visualization (tests added).
  • nice_circos() – Circos plot function for multi-omics circular visualization.
  • nice_GenomeTrack() – Genome track visualization with Ensembl-driven annotations and local annotation support.
  • Concordance functions – C-index and concordance metrics for model evaluation.

Fixes & Improvements

  • Offline-safe tests and local annotation fallback for nice_GenomeTrack().
  • Mocked biomaRt calls in get_annotations() tests for CI compatibility.
  • Stable Ensembl host pinned in get_annotation tests to avoid version drift.

Chores

  • Synced branch with upstream/dev via merge commit.

@DanielGarbozo DanielGarbozo merged commit 27dea6a into BigMindLab:dev May 19, 2026
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