online_trainings.md

Introduction

This page is our effort (Harvard Chan Bioinformatics Core or HBC) to curate training content available online for wet-bench biologists who want to learn bioinformatics. We have divided the content between general resources and content specific resources.

We created this list with help from many sources and conversations on Twitter. This list is not complete and we are thinking about this as a work in progress. We gratefully welcome all suggestions for expanding the list, so please update and create a pull request or email us with suggestions!

Table of contents

• Topic-specific online resources
  • R
  • Shell
  • Bulk RNA-seq
  • Single-cell RNA-seq
  • Chip-seq
• Other online resources
  • General topics
  • EdX/Coursera
  • Books/YouTube
  • Lists of resources from other sources

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Topic-specific online resources

R

• HBC's Introduction to R workshop
• R for Data Science book
• Data Carpentry's Introduction to R and RStudio for Genomics
• Rafa Irizarry's Introduction to Data Science (in R)

Shell

• HBC's Introduction to shell workshop
• Data Carpentry's Introduction to the Command Line for Genomics workshop

Bulk RNA-seq analysis

• HBC's Introduction to Bulk RNA-seq workshop (raw data to counts)
• HBC's Differential Gene Expression workshop (counts to DE and functional analysis)
• Mary Piper's DataCamp course RNA-Seq with Bioconductor in R
• Rafa Irizarry's RNA-seq Gene-Level Analysis (part of PH525X series Biomedical Data Science book)
• DESeq2's DGE analysis vignette
• EdgeR's DGE analysis vignette

Single-cell RNA-seq analysis

• HBC's Single-cell RNA-seq Analysis workshop
• Seurat vignettes
• Hemburg lab's Analysis of Single Cell RNA-seq Data course
• Pachter lab's "An introduction to single-cell RNA-seq"

ChIP-seq analysis

• HBC's ChIP-seq Analysis workshop
• Rafa Irizarry's ChIP-seq Analysis (part of PH525X series Biomedical Data Science book)

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Other online resources

General topics

• HBC's Short workshops
• List of online courses from Rafa Irizarry
• Learning R using online coding platform
• Learning Python using online coding platform
• Data carpentry workshops
• Software carpentry workshops
• Training from the Swiss Institute of Bioinformatics (SIB)
• Speciation Genomics Course covering basic R, variant calling/filtering, data visualization, and more

EdX/Coursera

• "Data Analysis for Life Science" with Rafa Irizarry
• "Principles, Statistical and Computational Tools for Reproducible Data Science" with Curtis Huttenhower, John Quackenbush et al.
• "Genomic Data Science Specialization" with James Taylor et al from Johns Hopkins University

Books/YouTube

• Online Book "Modern Statistics for Biology" by Susan Holmes and Wokfgang Huber
• "Bioinformatics Data Skills" by Vince Buffalo
• Videos explaining statistical concepts: Statquest with Josh Starmer

Lists of resources from other sources

• This Reddit thread has some good suggestions for wet-lab biologists

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