avalonmmiller / training-modules

Materials for short, half-day workshops

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.

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Summer-Fall 2022 Schedule (1pm - 4pm):

Topic and Link(s) to lessons	Prerequisites	Date	Registration
Basics of Python	None	8/10/2022	Closed
R practice exercises	Beginner R or Online R course - Harvard Catalyst	9/7/2022	Closed
Generating reports with Rmarkdown	Beginner R or Online R course - Harvard Catalyst	10/5/2022	Sign up!
Introduction to Shell	None	11/2/2022	Sign up!
Version control using Git/Github	Introduction to Shell	12/7/2022	Sign up!

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Links to workshop materials

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
[Introduction to the command-line interface]Intro_shell)	None
Intermediate bash	Beginner shell or Intro to the command-line interface
Version control using Git and Github	Beginner shell or Intro to the command-line interface
Accessing genomic reference and experimental sequencing data	Beginner shell or Intro to the command-line interface
Exploring genomic variants using GEMINI	Beginner shell or Intro to the command-line interface

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

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These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). 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.