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MICB 405 Bioinformatics: 2021.22

14 {DESeq2}: model fitting

14.1 Slides

You can download the slides for this tutorial below.

14.2 Learning outcomes

  • Describe properties of read count data and how DESeq models them.

  • Use R Markdown to create reproducible documents.

14.3 Setup

14.3.1 R packages

Install the R Markdown package.

install.packages("rmarkdown")

14.4 What is R Markdown?

R Markdown allows you to create reproducible documents containing code. It both includes the information on content and formatting information “markup”. R Markdown offers a simple way to markup your text using a simplified markup language called “Markdown”.

14.4.1 Formatting for emphasis

When you wrap a word or sentence with a single asterisk it gets emphasized, for example, *emphasis* becomes emphasis. Two asterisks create a strong emphasis, e.g. `strong emphasis is interpreted as strong emphasis.

14.4.2 Superscript and subsript

superscript^2^ superscript2

subscript~2~ subscript2

14.4.3 Linbreaks and paragraphs

A regular new line won’t render as a new line in the formatted document. Ending a line with two spaces creates a line break
like so. Leaving a blank line, creates a new paragraph.

This is a new paragraph.

14.5 Themes

Check out different Bootstrap themes. You can use them in the YAML header with theme: followed by default, cerulean, journal, flatly, darkly, readable, spacelab, united, cosmo, lumen, paper, sandstone, simplex, or yeti.