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We benchmark DAA strategies under complex confounding and batch effects, delivering robust pipelines and best practices for identifying differential microbes.

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Benchmarking Confounder-aware Differential Abundance (xConDA) Methods in Microbiome Data

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Introduction

We present a large-scale benchmark of 72 confounder-aware differential abundance analysis (DAA) strategies, assembled from six input schemes (five normalization approaches plus raw counts) and 14 statistical models.

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We benchmark DAA strategies under complex confounding and batch effects, delivering robust pipelines and best practices for identifying differential microbes.

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