Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data

[1] Shi P(2017)A model for paired-multinomial data and its application to analysis of data on a taxonomic tree Biometrics 73 1266-78

[2] Li H(2018)Generalized Hotelling’s test for paired compositional data with application to human microbiome studies Genet Epidemiol 42 459-69

[3] Zhao N(2014)Patterned progression of bacterial populations in the premature infant gut Proc Natl Acad Sci 111 12522-125274151715

[4] Zhan X(2018)q2-longitudinal: longitudinal and paired-sample analyses of microbiome data MSystems 3 e00219-18

[5] Guthrie KA(2018)The human gut microbiome in early-onset type 1 diabetes from the TEDDY study Nature 562 589-94

[6] Mitchell CM(2016)A two-part mixed-effects model for analyzing longitudinal microbiome compositional data Bioinformatics 32 2611-26175860434

[7] Larson J(2014)Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol 15 550-7

[8] La Rosa PS(2001)Fitting multivariate models to community data: a comment on distance-based redundancy analysis Ecology 82 290-4115

[9] Warner BB(2020)Testing hypotheses about the microbiome using the linear decomposition model (LDM) Bioinformatics 36 4106-8

[10] Zhou Y(1983)A nonstochastic interpretation of reported significance levels J Bus Econ Stat 1 292-6

[1] Shi P(2017)A model for paired-multinomial data and its application to analysis of data on a taxonomic tree Biometrics 73 1266-78

[2] Li H(2018)Generalized Hotelling’s test for paired compositional data with application to human microbiome studies Genet Epidemiol 42 459-69

[3] Zhao N(2014)Patterned progression of bacterial populations in the premature infant gut Proc Natl Acad Sci 111 12522-125274151715

[4] Zhan X(2018)q2-longitudinal: longitudinal and paired-sample analyses of microbiome data MSystems 3 e00219-18

[5] Guthrie KA(2018)The human gut microbiome in early-onset type 1 diabetes from the TEDDY study Nature 562 589-94

[6] Mitchell CM(2016)A two-part mixed-effects model for analyzing longitudinal microbiome compositional data Bioinformatics 32 2611-26175860434

[7] Larson J(2014)Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biol 15 550-7

[8] La Rosa PS(2001)Fitting multivariate models to community data: a comment on distance-based redundancy analysis Ecology 82 290-4115

[9] Warner BB(2020)Testing hypotheses about the microbiome using the linear decomposition model (LDM) Bioinformatics 36 4106-8

[10] Zhou Y(1983)A nonstochastic interpretation of reported significance levels J Bus Econ Stat 1 292-6