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compare_model version 1.0.0

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@wuwei77lx wuwei77lx released this 23 Sep 03:09
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v1.0.0
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Learn about vigilant mode.

Overview

Benchmarking of SCEG-HiC for predicting enhancer–gene links.

Contents

  • Model comparison:
    • Paired scATAC-seq/RNA-seq: Pearson, Spearman, CellOracle, DIRECT-NET, SCENIC+, FigR, and Signac.
    • scATAC-seq alone: Cicero, DIRECT-NET, Chi2+FDR, scEChIA, and Pearson.
    • ABC model: included for comparison, using bulk average Hi-C
  • Evaluation metrics: AUPRC and early precision; validated with cell type-specific Hi-C and eQTL datasets
  • Bulk average Hi-C: Bulk average Hi-C contact matrix generated to regularize peak–gene correlations via weighted graphical lasso

Notes

This release is archived on Zenodo and has a DOI: 10.5281/zenodo.17180859

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