index.Rmd

--- 
title: "Microbiome data science with R/Bioconductor"
subtitle: "Welcome to Radboud Summer School, July 2022"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [packages.bib]
biblio-style: apalike
link-citations: yes
github-repo: microbiome/course_2022_oulu
description: "Course material"
output:
  bookdown::gitbook
  bookdown::pdf_document2
always_allow_html: true  
classoption: oneside
geometry:
  - top=30mm
  - left=15mm
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo=TRUE, message=FALSE, warning=FALSE)
```

# Overview

<a href="https://bioconductor.org"><img src="`r rebook::BiocSticker('animated')`" width="200" alt="Bioconductor Sticker" align="right" style="margin: 0 1em 0 1em" /></a>


## Contents and learning goals

This course will focus on **microbiome data analysis
with R/Bioconductor**, a popular open source environment for
scientific data analysis. You will get an overview of the
reproducible data analysis workflows in microbiome research, with a
focus on gut-brain axis studies.

After the course you will know how to approach new tasks in the
analysis of taxonomic profiling data by taking advantage of available
documentation and R tools.

The teaching follows the open online documentation created by the
course teachers, extending the online book Orchestrating Microbiome
Analysis (https://microbiome.github.io/OMA). The openly licensed
teaching material will be available online during and after the
course, following Finnish national recommendations on open education.

The training material walks you through the standard steps of
biomedical data analysis covering data access, exploration, analysis,
visualization, reproducible reporting, and best practices in open
science.  We will teach generic data analytical skills that are
applicable to common data analysis tasks encountered in modern omics
research. The teaching format allows adaptations according to the
student's learning speed.


## Schedule and organizers

**Format** In-person course. For detailed schedule, see the
  [course
  website](https://www.ru.nl/radboudsummerschool/courses/2022/registration-longer-possible-brain-bacteria).

**Venue** University of Radboud. July 11-15, 2022.

**Expected background**

**Target audience** The course is primarily designed for advanced MSc
and PhD students, Postdocs, and biomedical researchers who wish to
learn new skills in scientific programming and biomedical data
analysis. Academic students and researchers encouraged to
apply. Priority will be given for local students. Some earlier
experience with R or another programming language is recommended. 

**Preparation** Advance preparation is expected. Online support is available. See section \@ref(start) for instructions.

## Acknowledgments

**Citation** We thank all [developers and contributors](https://microbiome.github.io) who have contributed open resources that supported the development of the training material. Kindly cite the course material as @radboud2022course 

**Contact** See [https://microbiome.github.io](https://microbiome.github.io)


**License and source code**

All material is released under the open [CC BY-NC-SA 3.0
License](LICENSE) and available online during and after the course,
following the [recommendations on open teaching
materials](https://avointiede.fi/fi/linjaukset-ja-aineistot/kotimaiset-linjaukset/oppimisen-ja-oppimateriaalien-avoimuuden-linjaus)
of the national open science coordination in Finland. The source code
of this repository is reproducible and contains the Rmd files with
executable code. See [README](README.md).