Resources:
MEG resources
- MEG bioinformatic term glossary
- AMR ++ pipeline overview
- Bioinformatic AMR and 16S pipeline overview
- Bioinformatics statistics overview
R programming
- RStudio cheatsheets
- This website has tons of helpful cheatsheets for various R packages and analyses methods. Also includes cheatsheets translated to other languages.
- YaRrr! The Pirate’s Guide to R
- This is a free online book that goes over many useful topics in a quirky, but fun way! Follow along with our simplified R scripts in Lesson 1 and reference this book if you have any other questions.
- R programming coursera course
- This free coursera course goes in-depth with all of the functionality of R. It combines videos with example R scripts for you to follow along with. We recommend this course after you have been playing around with R a bit and want to learn more about the details into how R works.
- Introduction to R workshop
- We haven't personally tried this workshop, but they have a combination of videos, slides, and R code for various topics.
Data visualization
- dataviz project
- This website is for a private company, but they have a great interface for exploring different figure types
- Visual vocabulary
- Handy outline and explanation for the uses of different plots.
- You can also check out this interactive figure of the same material
- FT Visual Journalism Team
- Awesome site with articles covering various topics and with the emphasis on creating awesome graphics to convey
- Interactive Jupyter notebooks
Command-line
- Explain shell
- cool website that explains bash commands piece by piece
Statistics
- GUide to STatistical Analysis in Microbial Ecology (GUSTA ME)
- LHS 610: Exploratory Data Analysis for Health
- We haven't personally tried this course, but they provide great videos and code examples for learning how to explore data using R.
- #bioinformatics live twitter feed
- R-specific resources
- ggpubr
- Nice package for "publication-ready" figures.
- Harvard's Data Science: R Basics
- Collaborative spreadsheet of resources
- Choose the right test
- ggpubr
- Batch effects
- Tackling the widespread and critical impact of batch effects in high-throughput data
- Why Batch Effects Matter in Omics Data, and How to Avoid Them
- Beware the bane of batch effects
- Mitigating the adverse impact of batch effects in sample pattern detection
- Identifying and mitigating batch effects in whole genome sequencing data
- Why Batch Effects Matter in Omics Data, and How to Avoid Them