Entry 3.1: RMarkdown Basics - bcb420-2025/Chloe_Calica GitHub Wiki

Background

I have used RMarkdown before so I'm familliar with some of the concepts shown in the RMarkdown Tips lecture. However, I haven't really explored it much further than the basics which is why I found it interesting that there are other features such as the table of contents and bibliography that can be added to RMarkdown files.

RMarkdown Cheatsheet

  • This the cheatsheet link from the RMarkdown website.
  • I also generated my own template below for ease of use in further assignments:
---
title: "BCB420 - Computational Systems Biology"
subtitle: "RMarkdown Template"
author: "Chloe Nichole Calica"
date: "r Sys.Date()"
output:
  html_document:
    toc: true
    toc_depth: 2
bibliography: references.bib
csl: biomed-central.csl
---

Notes

  • Headings are specified with # and depth will vary by the number of # specified.
  • To add references in text, use the @ sign followd by the name of the reference. Dont' forget to add the bibtex of the article in the references.bib file.
  • Code Chunk Specifications:
    • eval - evaluate code and include results
    • echo - display code with results
    • warning - display warnings
    • error - (default: false) display errors
    • message - display message