Some R packages I find useful:
- vegan (great statistics functions for community ecology data analysis)
- microeco (wrapper for microbial ecology data analysis using meco data)
- file2meco (phyloseq/qiime to meco conversion)
- ggpicrust2 (PICRUSt2 output analysis & visualization made easy)
- fantaxtic (nested bar plots for phyloseq data)
- maaslin3 (microbiome multivariate association with linear models)
- QIIME2: How to train a taxonomic classifier
- QIIME2: How to merge feature table w/ resp. taxonomic assignments
- QIIME2: How to merge different feature tables
- QIIME2: Amplicon read processing (incl. PICRUSt2)
- QIIME2: Processed read files export (f: R/phyloseq)
- QIIME2: Calculate diversity metrics & run some statistics
Work in progress...