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‎Atlas.Rmd

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@@ -4,7 +4,11 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
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number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Betadiversity.Rmd

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bibliography:
55
- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

‎Betadiversity.html

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‎Bimodality.Rmd

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@@ -4,7 +4,11 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
55
- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Clustering.Rmd

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@@ -4,7 +4,11 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Comparisons.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Composition.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
11+
toc_float: true
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self_contained: true
9-
thumbnails: false
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

‎CompositionAmplicondata.Rmd

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bibliography:
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- bibliography.bib
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output:
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rmdformats::readthedown:
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BiocStyle::html_document:
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number_sections: no
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toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎CompositionAmplicondata2.Rmd

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bibliography:
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- bibliography.bib
66
output:
7-
rmdformats::readthedown:
8-
self_contained: false
7+
BiocStyle::html_document:
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number_sections: no
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toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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mathjax: local
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

‎Contributing.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Core.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎CoremicrobiotaAmplicon.Rmd

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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddockoutput:
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rmdformats::readthedown:
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self_contained: true
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thumbnails: false
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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---
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<!--

‎DMM.Rmd

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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Data.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
11+
toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Diversity.Rmd

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@@ -4,13 +4,17 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

‎Experimental.Rmd

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bibliography:
55
- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎HITChip.Rmd

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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Heatmap.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Installation.Rmd

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bibliography:
55
- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
11+
toc_float: true
812
self_contained: true
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

‎Interactive.Rmd

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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Landscaping.Rmd

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bibliography:
55
- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Mixedmodels.Rmd

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@@ -4,7 +4,11 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Negativebinomial.Rmd

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@@ -4,7 +4,11 @@ author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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bibliography:
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- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Networks.Rmd

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bibliography:
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- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
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toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Ordination.Rmd

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bibliography:
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- bibliography.bib
66
output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
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self_contained: true
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thumbnails: true
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lightbox: true

‎Output.Rmd

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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
11+
toc_float: true
812
self_contained: true
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thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
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highlight: haddock
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---
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highlight: haddock ---
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<!--
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteIndexEntry{microbiome tutorial - output}

‎PERMANOVA.Rmd

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bibliography:
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- bibliography.bib
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output:
7-
rmdformats::readthedown:
7+
BiocStyle::html_document:
8+
number_sections: no
9+
toc: yes
10+
toc_depth: 4
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toc_float: true
812
self_contained: true
913
thumbnails: true
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lightbox: true
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gallery: true
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use_bookdown: false
13-
highlight: haddock
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highlight: haddock
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---
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<!--
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%\VignetteEngine{knitr::rmarkdown}

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