In June 2020, I started to learn how to (properly!) compute the microbiome data.
Here, I'm collecting online resources that made this learning journey easier and fun.
WIP: Still learning and updating this collection! If you have some of your favourite bioinformatics learning material, feel free to let me know.
KUDOS to all bioinformaticians and computational scientists who are sharing their knowledge!
✅ PARTICULARLY worked for me
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✅ Code Club by @PatSchloss
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✅ Modern Statistics for Modern Biology by @SherlockpHolmes and @wolfgangkhuber
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Biostar Handbook by István Albert
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Bioinformatics data skills by @vsbuffalo
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Examples from Practical computing for biologists by @caseywdunn @beroe
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The Missing Semester of Your CS Education by @anishathalye @jonhoo @jjgort
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Python Scripting for Computational Molecular Science by @jessica_a_nash @ARingerMcDonald
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Canadian Bioinformatics Workshops by @Bioinfodotca *Past workshop content is available under a Creative Commons License here or here.
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Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau and Pavel Pevzner
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Rosalind exercises
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2021 Microbiome Informatics Webinars by OSU Center of Microbiome Science
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Bioinformatics Workbook A tutorial to help scientists design their projects and analyze their data.
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An Introduction to Applied Bioinformatics by Gregory Caporaso.
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✅ Metagenomics tools etc. by Big Data Biology Lab.
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🇪🇸 Bioinformática Microbiana by Bruno Gómez Gil and Abraham Guerrero.
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🇪🇸 Genomas a partir de metagenomas by Diana Hernández Oaxaca and Mirna Rosas Vázquez Landa.
PLUS, check out this list of bioinformatics books here,
📻 podcasts:
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✅ The bioinformatics chat produced by Roman Cheplyaka and hosted by Roman and Jacob Schreiber
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The Bioinformatics and Beyond Podcast by Leo Elworth and Ep: Wet Lab / Dry Lab Transitioning with Dr. Willian da Silveira
& What is a bioinformatics postdoc? The experienced bioinformaticians Fatemeh Vafaee, Matt Field, Nikeisha Caruana, Philipp Bayer, Thomas Quinn, Ignatius Pang answering questions such as:
What is a bioinformatics postdoc?
Tips for landing a postdoc position?
Finding a mentor?
What are the challenges?
How to handle these challenges?
A cartoon guide to bioinformatics by a novice coder by Ed Himelblau
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The Missing Semester of Your CS Education by @anishathalye @jonhoo @jjgort
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UNIX crash course by @AstrobioMike
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✅ Git for Scientists by Simon Cockell
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Learn Git Branching - the most visual and interactive way to learn Git on the web.
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Understand how to write a good commit message through memes 😉 by Hritik Jaiswal
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Bioconductor for Genomic Data Science by Kasper Daniel Hansen
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Introduction to Data Science: Data Wrangling and Visualization with R by Rafael Irizarry
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Introduction to Data Science: Statistics and Prediction Algorithms Through Case Studies by Rafael Irizarry
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✅ Biology meets Programming - Introduction to Bioinformatics using Python by deNBI
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30 Days of Python by Justin Mitchel *first 8 lessons
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✅ LxMLS2020 Intro to Python by Luis Pedro Coelho
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Exploring and understanding Python through surprising snippets What the f*ck Python! 😱
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✅ Tips & tricks for large scale processing with Python by Big Data Biology Lab
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A visual introduction to machine learning by @stephaniejyee and @tonyhschu
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How to Critically Evaluate Machine Learning Methods by @tpq__
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A guide to machine learning for biologists by Greener, J.G., Kandathil, S.M., Moffat, L. et al. Nat Rev Mol Cell Biol (2021)
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Machine Learning for Biology ml4bio-workshop