| Basic Metagenomics Workflow |
Phinch |
swirl (learn R) |
| Basic Genomics Workflow |
QIIME 2 |
Cookbook for R (book - graphics with ggplot2) |
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MiGA online (id and check completeness of MAGs) |
Start here with Amplicons |
Fundamentals of Data Visualization (book - making the best figures) |
| antiSMASH |
minimalR: tutorials from Schloss lab on making common microbiome figures in R |
R for Data Science (book - using the "tidyverse") |
| BiG-SCAPE |
DADA2 Tutorial |
R Color Palettes and Point Shapes (JM's tips) |
| workflow for metagenomes in anvi'o |
Phyloseq Tutorials |
R Color Palettes: National Park Posters version |
| Meren lab's Intro to Microbial 'Omics |
Sorting Samples by Metadata |
cowplot (for multi-panel ggplot2 figures) |
| anvi'o metagenomics tutorial |
Get abundant Taxa |
patchwork (also for multi-panel ggplot2 figures) |
| anvi'o - all programs/scripts |
Phyloseq Object to LEfSe |
RStudio Cheatsheets |
| Anvi'o Pangenomic Workflow |
LEfSe on Galaxy |
Julie's R tricks |
| BioBakery - Huttenhower lab |
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