Functional microbiomic approaches using lower airway samples identify a subset of lung microbial communities with evidence of active microbial metabolism

Manuscript Analysis

Prerequisites

• MacOS/Windows/Linux
• R (version 3.5.1)

Installing R [typical time = 5-10 minutes]

1. Open an internet browser and go to www.r-project.org.
2. Click the "download R" link in the middle of the page under "Getting Started."
3. Select a CRAN location (a mirror site) and click the corresponding link.
4. Click on the "Download R for [your operating system]" link at the top of the page.
5. Click on the file containing the latest version of R under "Files."
6. Save the .pkg file, double-click it to open, and follow the installation instructions.

Running the Analysis

There are nine seperate analysis pipelines:

• Human 16S rRNA gene Sequencing
• Human Whole Genome Sequencing
• Human RNA Metatranscriptome Sequencing
• Gene Set Enrichment Analysis
• PROCRUSTES Analysis
• MultiOmic Analysis
• Correlation Anslysis
• Mouse 16S rRNA gene Sequencing
• Mouse RNA Metatranscriptome Sequencing