Current Topics in Bioinformatics workshops

Audience Computational Skills Duration
Biologists Beginner or intermediate R and/or beginner bash 2-3 hour workshops

Use https://tinyurl.com/hcbc-modules to access this page.

This repository has teaching materials for 2-3 hour, hands-on workshops covering a variety of topics related to bioinformatics data analysis. The workshops will lead participants through performing different types of analyses using R/RStudio or Linux.

Some workshops will require a working knowledge of R or completion of the Introduction to R workshop. Other workshops will require a working knowledge of the bash scripting language or completion of the Introduction to Shell workshop.

** NOTE: Detailed information and preparation instructions for each of the workshops can be found by clicking on the workshop links in the table below.

Workshop introduction slides are available here.

Current Topics in Bioinformatics workshops Winter 2025 Schedule (1pm - 4pm):

Tools for Transparent Research - Hands-On with Git & RMarkdown

Topic and Link(s) to lessons Prerequisites Date Registration
R Basics None 2/19/2025 Closed
Markdown for Reproducible Reporting R Basics 3/19/2025 Sign up!
“Track Changes” for your code: An Introduction to Git and GitHub None 4/16/2025 Sign up!
Coding with others: Managing conflicts on GitHub “Track Changes” for your code: An Introduction to Git and GitHub 5/21/2025 Sign up!

R-based workshops:

Topic and Link(s) to lessons Prerequisites
Introduction to R None
Tidyverse Beginner R or Intro to R workshop
Introduction to R Practical Beginner R or Completion of the Intro to R online resource
Gene annotations and functional analysis of gene lists Beginner R or Intro to R workshop
Generating research analysis reports with RMarkdown Beginner R or Intro to R workshop
Interactive Data Visualization with Shiny in R (with Ista Zahn from the Harvard Business School) Beginner R or Intro to R workshop
Publication Perfect: Part I Beginner R or Completion of the Intro to R online resource
Publication Perfect: Part II Publication Perfect: Part I
Functional analysis of gene lists Beginner R or Intro to R workshop

Shell-based workshops:

Topic and Link(s) to lessons Prerequisites
Basic Shell/Introduction to the command-line interface None
Accelerate with Automation - Making your code work for you The Foundation - Basic Shell
Needle in a Haystack - Finding and summarizing data from colossal files The Foundation - Basic Shell
Shell Tips and Tricks on O2 The Foundation - Basic Shell
Version control using Git and Github The Foundation - Basic Shell
Accessing genomic reference and experimental sequencing data The Foundation - Basic Shell
Exploring genomic variants using GEMINI The Foundation - Basic Shell

Additional workshops:

Topic and Link(s) to lessons Prerequisites
Introduction to Python None
Planning a bulk RNA-seq analysis: Part I None
Planning a bulk RNA-seq analysis: Part II None
Make your (RNA-seq) data analysis reproducible- Taught by Julie Goldman from Countway Library None
Improving your (RNA-seq) data analysis using version control (Git) None
Introduction to scRNA-seq and data pre-processing R Basics and Basic Shell

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC) RRID:SCR_025373. These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

A lot of time and effort went into the preparation of these materials. Citations help us understand the needs of the community, gain recognition for our work, and attract further funding to support our teaching activities. Thank you for citing the corresponding course (as suggested in its “Read Me” section) if it helped you in your data analysis.