A Minimal Book Example
1
Prerequisites
2
Fig 3
2.1
3B: stacked bar chart.
2.2
3C: alpha and beta diversity between CART patients and healthy volunteers
2.2.1
alpha diversity (Simpson’s reciprocal)
2.2.2
beta diversity (PCOA of Bray-Curtis)
2.3
Fig 3 E&F Lefse analysis with taxa abundance at ASV level
2.4
Fig 3D Bayesian modeling with microbiome alpha diversity as predictor
2.4.1
outcome: toxicity
2.4.2
outcome : CR_d100
2.5
Fig 3G Bayesian modeling with 5 genera abundance as predictor(outcome CR)
2.6
Fig3H Histogram to illustrate the predicted probability of day100 CR
2.7
Fig 3I Bayesian modeling with 5 genera abundance as predictor(outcome toxicity)
2.8
Fig3J Histogram to illustrate the predicted probability of toxicity
2.9
Fig 3K lefse of pathway abundance using shotgun data
References
Published with bookdown
CART microbiome analysis
CART microbiome analysis
Anqi Dai
2021-09-27
Chapter 1
Prerequisites
install.packages
(
"bookdown"
)