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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.

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

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.