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index.Rmd
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---
title: "Introduction to the microbiome R package"
author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
bibliography:
- bibliography.bib
csl: ieee.csl
output:
BiocStyle::html_document:
number_sections: no
toc: yes
toc_depth: 4
toc_float: true
self_contained: true
thumbnails: true
lightbox: true
gallery: true
use_bookdown: false
highlight: haddock
---
<!--
%\VignetteIndexEntry{microbiome tutorial}
%\VignetteEngine{knitr::rmarkdown}
%\usepackage[utf8]{inputenc}
%\VignetteEncoding{UTF-8}
-->
```{r, echo=FALSE, message=FALSE, warning=FALSE}
# Handle citations
require(knitcitations)
require(bookdown)
# cleanbib()
# options("citation_format" = "pandoc")
bib <- read.bibtex("bibliography.bib")
#opts_chunk$set(fig.width=4, fig.height=3, par=TRUE, out.width='2in', fig.pos='H')
library(knitr)
knitr::opts_chunk$set(fig.path = "figure/", dev="CairoPNG")
#----------------------------
# CSS Style
### Import the style from CSS file 'css_path'
style <- paste(readLines("bioc.css"), collapse = "\n")
opts_knit$set(self.contained = TRUE,
upload.fun = image_uri, ## optional
header = c(highlight = style))
```
[](https://travis-ci.org/microbiome/microbiome)
[](https://gitter.im/microbiome/microbiome?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[](https://codecov.io/github/microbiome/microbiome?branch=master)
Tools for microbiome analysis; with multiple example data sets from published studies; extending the [phyloseq](http://joey711.github.io/phyloseq/import-data) class. The package is in [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/microbiome.html) and aims to provide a comprehensive collection of tools and tutorials, with a particular focus on amplicon sequencing data.
# Getting started
* [Overview (vignette)](https://bioconductor.org/packages/devel/bioc/vignettes/microbiome/inst/doc/vignette.html)
* [Installation](Installation.html)
* [Example data](Data.html)
* [Data operations](Preprocessing.html) (subsetting, transformations etc.)
# Microbiome analysis
* [Alpha diversity](Diversity.html)
* [Beta diversity / Community heterogeneity](Betadiversity.html)
* [Community composition](Composition.html)
* [Core microbiota](Core.html)
* [Dirichlet Multinomial Mixtures (DMM) for community typing](DMM.html)
* [Dissimilarity-Overlap Analysis (DOC)](DOC.html)
* [Landscapes](Landscaping.html) (population density analysis)
* [Stability and tipping elements](Stability.html)
# Visualization and related
* [Heatmaps](Heatmap.html)
* [Ordination](Ordination.html) (PCA, PCoA, NMDS, RDA etc.)
* [Regression](Regression.html)
* [Generating output files/figures](Output.html)
# Statistical analysis
* [Association analysis](Heatmap.html)
* [Bimodality](Bimodality.html)
* [Community comparisons](Comparisons.html) ([limma](limma.html), [PERMANOVA](PERMANOVA.html), [mixed models](Mixedmodels.html), [negative binomial](Negativebinomial.html) etc)
# Tutorial workflows
* [Analysis of gut microbiota in 1006 western adults](Tutorial.html)
* [Univariate tests for two-group comparison](all.html)
# Development
New examples, tutorial pages, and other contributions are [welcome](Contributing.html). The material can be freely used, modified and distributed under the [Two-clause FreeBSD license](http://en.wikipedia.org/wiki/BSD\_licenses). For source code, see the [Github page](https://github.com/microbiome/microbiome/).
# Contribute
Contributions are welcome:
* [Issue Tracker](https://github.com/microbiome/microbiome/issues)
* [Pull requests](https://github.com/microbiome/microbiome/)
* Subscribe to the [mailing list](https://groups.google.com/forum/#!forum/microbiome-devel) ([email protected])
* [Star us on the Github page](https://github.com/microbiome/microbiome)
## Contibuting new tutorials or examples
We welcome new examples and tutorials to be added in this collection, and will fully acknowledge such contributions.
You can modify one of the existing examples (.html) and make a pull request. Or, you can propose a new tutorial page. The Rmarkdown source code (..html) for all [tutorials](http://microbiome.github.io/tutorials/) is available in the Github [index.page](https://github.com/microbiome/tutorials). Fork the repository, clone it, modify the tutorials, and make a pull request.
# Acknowledgements
**Kindly cite this work** as follows: "Leo Lahti, Sudarshan Shetty [et al.](https://github.com/microbiome/microbiome/graphs/contributors) (2017). Tools for microbiome analysis in R. Version `r sessionInfo()$otherPkgs$microbiome$Version`. URL: [http://microbiome.github.com/microbiome](http://microbiome.github.com/microbiome). Check also the relevant references listed in the manual page of each function.
The package utilizes tools from a number of other R extensions, including dplyr `r citep(bib[["Wickham_2017"]])`, ggplot2 `r citep(bib[["Wickham_2009"]])`, phyloseq `r citep(bib[["McMurdie_2013"]])`, tidyr `r citep(bib[["Wickham_2017a"]])`, vegan `r citep(bib[["Oksanen_2017"]])`.
This website theme was created by modifiying the [rmdformats](https://github.com/juba/rmdformats) **readthedown** format.
```{r, echo=FALSE, message=FALSE}
#You can embed citations, for example: `r citep(bib[["lahti14natcomm"]])`
#You can embed citations, for example2: @lahti14natcomm
#Cite with DOI: `r citep("10.1890/11-0011.1")`
#Cite URL `r citep("http://knowledgeblog.org/greycite")`
#For automated markdown citations, check [this](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html), [this](https://github.com/cboettig/knitcitations), and [this](http://www.carlboettiger.info/2012/03/24/citations-in-markdown-using-knitr.html).
# write.bibtex(file="references.bib")
```
```{r, echo=FALSE, message=FALSE, results='asis'}
# bibliography(style="html")
```