Programs

• RStudio: statistical computing and graphics
• Galaxy: open source, web-based platform for data intensive biomedical research
• QIIME: Quantitative Insights Into Microbial Ecology​ ​
• Bioconductor
• ​MG-RAST

Datasets

• Personal Genome Project (Microbiome)
• ​Human Microbiome Project (NIH)
• NCBI Pathogen Detection. Bacterial pathogen genomic sequences originating in food, environmental sources, and patients
  

Tutorials
RStudio

• Plotting in R for Biologists -- Lesson 1: From data to plot with a few magic words
• ​Plotting in R for Biologists -- Lesson 2: Importing data from excel or text files

Galaxy

• Galaxy Project ​
• Galaxy: Metagenomic Example​ ​

Resources

• R for Bioinformatics: Wellcome Trust Sanger Institute
• Plotting in R for Biologists - Datasets, scripts, and video files

Metagenomic Datasets

• JGI: Integrated Microbial Genomes and Microbial Samples