Bioinformatics Training Resources for Experimentalists (and Friends)

Links updated January 10, 2024

There are now so many excellent courses and freely available resources for learning bioinformatics it can be hard to know where to start. Some of our favourite introductory resources come from the Genomic Data Science specialization on Coursera, and from the Canadian Bioinformatics Workshops series. Here we have organized available content by level of expertise and by interest. We take no responsiblity (or credit) for the content of the linked materials, though I think they are all quite good and reflect a lot of thought and hard work by the content authors. At the bottom we include a couple of courses and resources suitable for someone with a computational background who wants an entrez to bioinformatics and biology more broadly.

Jason de Koning
Cumming School of Medicine
University of Calgary
With thanks to: Dr. Quan Long and Dr. Paul Gordon for input

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Foundations

I want to start with the basics (what are genomics, data, bioinformatics):

• Introduction to Genomic Technologies (Coursera)

I want to learn about basic bioinformatics tools and approaches:

• Bioinformatics Methods I (BLAST, align, phylogeny, RNA-seq, etc.) Coursera
• High Throughput Genomics Analysis (CBW 2018)

I want to learn how to use tools and workflows without coding:

• Genomic Data Science with Galaxy (Coursera)
• EnsEMBL BioMart (web-based querying of huge databases easily) Short Tutorial

I want to learn how to run tools at the command-line:

• Command Line Tools for Genomic Data Science (Coursera)

I want to learn some statistics relevant to bioinformatics:

• Statistics for Genomic Data Science (Coursera)

I want to learn to code:

• Python for Genomic Data Science (Coursera)
• Algorithms for DNA Sequencing (intro. to basic algorithms and data structures) (Coursera)

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Intermediate

I want to learn to use R and Bioconductor:

• Introduction to R (CBW)
• Exploratory Analysis of Biological Data (CBW)
• Bioconductor for Genomic Data Science (Coursera)

I want to learn bioinformatics tools for a specific task or domain:

• Informatics for RNA-seq Analysis (CBW)
• Microbiome Analysis (CBW)
• Epigenomic Data Analysis (CBW)
• Bioinformatics for Cancer Genomics (CBW)
• Infectious Disease Genomic Epidemiology (CBW)

I want to apply more advanced methods to research problems:

• Pathway and Network Analysis of -Omics Data (CBW)

I want some bioinformatics and programming problem sets and/or resources for problem-based learning:

• Rosalind (web)

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Advanced

I have a computational background and want to learn some computational biology:

• Computational Biology (Kellis) MIT course
• Computational Genomics: Applied Comparative Genomics (Schatz) Course
• Applied Computational Genomics (Quinlan) Course

I want some in depth resources for next steps and other topics:

• Introduction to Java Programming (Ebook)
• Deep Learning (theory and deep background) (Ebook)

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Biology for Computer Scientists

I have a computational background and want to learn some biology relevant to genomics:

• Introduction to Genomic Technologies (Coursera)
• XBio iBiology (Web)
• Algorithms for DNA Sequencing (intro. to basic algorithms and data structures; Coursera)