├── .gitignore ├── Managing_batch_effects ├── 01-Batch_effect_detection.Rmd ├── 02-Batch_effect_adjustment.Rmd ├── 03-Methods_evaluation.Rmd ├── 04-Simulations.Rmd ├── 05-Bibliography.Rmd ├── Functions.R ├── _bookdown.yml ├── _bookdown_files │ └── Managing_batch_effects_files │ │ ├── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-10-2.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-12-2.png │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-15-2.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-17-2.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-18-2.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-19-2.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-44-1.png │ │ ├── unnamed-chunk-44-2.png │ │ ├── unnamed-chunk-44-3.png │ │ ├── unnamed-chunk-44-4.png │ │ ├── unnamed-chunk-44-5.png │ │ ├── unnamed-chunk-44-6.png │ │ ├── unnamed-chunk-45-1.png │ │ ├── unnamed-chunk-45-2.png │ │ ├── unnamed-chunk-46-1.png │ │ ├── unnamed-chunk-46-2.png │ │ ├── unnamed-chunk-46-3.png │ │ ├── unnamed-chunk-46-4.png │ │ ├── unnamed-chunk-46-5.png │ │ ├── unnamed-chunk-46-6.png │ │ ├── unnamed-chunk-46-7.png │ │ ├── unnamed-chunk-47-1.png │ │ ├── unnamed-chunk-47-2.png │ │ ├── unnamed-chunk-49-1.png │ │ ├── unnamed-chunk-49-2.png │ │ ├── unnamed-chunk-51-1.png │ │ ├── unnamed-chunk-51-2.png │ │ ├── unnamed-chunk-56-1.png │ │ ├── unnamed-chunk-56-2.png │ │ ├── unnamed-chunk-58-1.png │ │ ├── unnamed-chunk-58-2.png │ │ ├── unnamed-chunk-63-1.png │ │ ├── unnamed-chunk-64-1.png │ │ ├── unnamed-chunk-66-1.png │ │ ├── unnamed-chunk-66-2.png │ │ ├── unnamed-chunk-67-1.png │ │ ├── unnamed-chunk-67-2.png │ │ ├── unnamed-chunk-68-1.png │ │ ├── unnamed-chunk-69-1.png │ │ ├── unnamed-chunk-7-1.png │ │ ├── unnamed-chunk-71-1.png │ │ ├── unnamed-chunk-72-1.png │ │ ├── unnamed-chunk-75-1.png │ │ ├── unnamed-chunk-77-1.png │ │ ├── unnamed-chunk-79-1.png │ │ ├── unnamed-chunk-8-1.png │ │ ├── unnamed-chunk-81-1.png │ │ ├── unnamed-chunk-83-1.png │ │ ├── unnamed-chunk-84-1.png │ │ ├── unnamed-chunk-85-1.png │ │ ├── unnamed-chunk-86-1.png │ │ ├── unnamed-chunk-87-1.png │ │ ├── unnamed-chunk-88-1.png │ │ ├── unnamed-chunk-89-1.png │ │ └── unnamed-chunk-9-1.png │ │ └── figure-latex │ │ ├── unnamed-chunk-10-1.pdf │ │ ├── unnamed-chunk-10-2.pdf │ │ ├── unnamed-chunk-12-1.pdf │ │ ├── unnamed-chunk-12-2.pdf │ │ ├── unnamed-chunk-15-1.pdf │ │ ├── unnamed-chunk-15-2.pdf │ │ ├── unnamed-chunk-17-1.pdf │ │ ├── unnamed-chunk-17-2.pdf │ │ ├── unnamed-chunk-18-1.pdf │ │ ├── unnamed-chunk-18-2.pdf │ │ ├── unnamed-chunk-19-1.pdf │ │ ├── unnamed-chunk-19-2.pdf │ │ ├── unnamed-chunk-20-1.pdf │ │ ├── unnamed-chunk-21-1.pdf │ │ ├── unnamed-chunk-22-1.pdf │ │ ├── unnamed-chunk-44-1.pdf │ │ ├── unnamed-chunk-44-2.pdf │ │ ├── unnamed-chunk-44-3.pdf │ │ ├── unnamed-chunk-44-4.pdf │ │ ├── unnamed-chunk-44-5.pdf │ │ ├── unnamed-chunk-44-6.pdf │ │ ├── unnamed-chunk-45-1.pdf │ │ ├── unnamed-chunk-45-2.pdf │ │ ├── unnamed-chunk-46-1.pdf │ │ ├── unnamed-chunk-46-2.pdf │ │ ├── unnamed-chunk-46-3.pdf │ │ ├── unnamed-chunk-46-4.pdf │ │ ├── unnamed-chunk-46-5.pdf │ │ ├── unnamed-chunk-46-6.pdf │ │ ├── unnamed-chunk-46-7.pdf │ │ ├── unnamed-chunk-47-1.pdf │ │ ├── unnamed-chunk-47-2.pdf │ │ ├── unnamed-chunk-49-1.pdf │ │ ├── unnamed-chunk-49-2.pdf │ │ ├── unnamed-chunk-51-1.pdf │ │ ├── unnamed-chunk-51-2.pdf │ │ ├── unnamed-chunk-56-1.pdf │ │ ├── unnamed-chunk-56-2.pdf │ │ ├── unnamed-chunk-58-1.pdf │ │ ├── unnamed-chunk-58-2.pdf │ │ ├── unnamed-chunk-63-1.pdf │ │ ├── unnamed-chunk-64-1.pdf │ │ ├── unnamed-chunk-66-1.pdf │ │ ├── unnamed-chunk-66-2.pdf │ │ ├── unnamed-chunk-67-1.pdf │ │ ├── unnamed-chunk-67-2.pdf │ │ ├── unnamed-chunk-68-1.pdf │ │ ├── unnamed-chunk-69-1.pdf │ │ ├── unnamed-chunk-7-1.pdf │ │ ├── unnamed-chunk-71-1.pdf │ │ ├── unnamed-chunk-72-1.pdf │ │ ├── unnamed-chunk-75-1.pdf │ │ ├── unnamed-chunk-77-1.pdf │ │ ├── unnamed-chunk-79-1.pdf │ │ ├── unnamed-chunk-8-1.pdf │ │ ├── unnamed-chunk-81-1.pdf │ │ ├── unnamed-chunk-83-1.pdf │ │ ├── unnamed-chunk-84-1.pdf │ │ ├── unnamed-chunk-85-1.pdf │ │ ├── unnamed-chunk-86-1.pdf │ │ ├── unnamed-chunk-87-1.pdf │ │ ├── unnamed-chunk-88-1.pdf │ │ ├── unnamed-chunk-89-1.pdf │ │ └── unnamed-chunk-9-1.pdf ├── _output.yml ├── book.bib ├── datasets │ └── microbiome_datasets.RData ├── figures │ └── table.png ├── index.Rmd ├── logo-unimelb.png ├── packages.bib ├── preamble.tex └── style.css ├── README.md └── docs ├── Managing_batch_effects.pdf ├── Managing_batch_effects.tex ├── Managing_batch_effects_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-10-2.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-12-2.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-15-2.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-17-2.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-18-2.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-19-2.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-45-1.png │ ├── unnamed-chunk-45-2.png │ ├── unnamed-chunk-47-1.png │ ├── unnamed-chunk-47-2.png │ ├── unnamed-chunk-49-1.png │ ├── unnamed-chunk-49-2.png │ ├── unnamed-chunk-51-1.png │ ├── unnamed-chunk-51-2.png │ ├── unnamed-chunk-56-1.png │ ├── unnamed-chunk-56-2.png │ ├── unnamed-chunk-58-1.png │ ├── unnamed-chunk-58-2.png │ ├── unnamed-chunk-63-1.png │ ├── unnamed-chunk-64-1.png │ ├── unnamed-chunk-66-1.png │ ├── unnamed-chunk-66-2.png │ ├── unnamed-chunk-67-1.png │ ├── unnamed-chunk-67-2.png │ ├── unnamed-chunk-68-1.png │ ├── unnamed-chunk-69-1.png │ ├── unnamed-chunk-7-1.png │ ├── unnamed-chunk-71-1.png │ ├── unnamed-chunk-72-1.png │ ├── unnamed-chunk-75-1.png │ ├── unnamed-chunk-77-1.png │ ├── unnamed-chunk-79-1.png │ ├── unnamed-chunk-8-1.png │ ├── unnamed-chunk-81-1.png │ ├── unnamed-chunk-83-1.png │ ├── unnamed-chunk-84-1.png │ ├── unnamed-chunk-85-1.png │ ├── 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