FrederickHuangLin/Microbiome-Review-Code-Archive FrederickHuangLin/Microbiome-Review-Code-Archive

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FrederickHuangLin/Microbiome-Review-Code-Archive
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FrederickHuangLin

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Repository Details

Data, scripts, and outputs for the npj Biofilms and Microbiomes paper "Analysis of microbial compositions: A review of normalization and differential abundance analysis"

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ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data
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ANCOM-Code-Archive

Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.
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ANCOM-BC-Code-Archive

Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.
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SECOM-Code-Archive

Archive: Data, scripts, and outputs for the paper "Sparse Estimation of Correlations among Microbiomes (SECOM)". Please check our ANCOMBC R package for the most up-to-date SECOM functions.
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Gut-Microbiome-and-HIV-Infection

Scripts and outputs for the paper "Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM"
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ANCOM-BC2-Code-Archive

Archive: Data, scripts, and outputs for the paper "Multi-group Analysis of Compositions of Microbiomes with Covariate Adjustments and Repeated Measures". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.
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Gut-Microbiome-and-Sexual-Behavior

Scripts and outputs for the paper "High risk sexual behavior is linked to changes in gut microbiome and systemic inflammation that lead to HIV-1 infection in men who have sex with men"
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Gut-Microbiome-and-Metabolic-Syndrome

The archive for data, scripts, and outputs for the paper "Bacterial and Immunological Mediators linking Caregiving with Metabolic Syndrome".
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