Manuscript Analysis

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

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.

• UpStream Processing
• Metagenome
• Metatranscriptome
• MultiOMICS
• Human RNA Transcriptome

The Required Input Data

• Microbe Abundance (no-miss-table-dada2.qza):An abundance table with microbial species in rows and samples in columns.
• Taxonomy Table (taxonomy.qza): Table of the taxonomic annotation
• MetaData (BX_Sputum_convert.txt): A spreadsheet with samples in rows and metadata in columns
• Tree File (rooted-tree_quality.qza):

1. Open R
2. Follow Code Bronchiectasis.Neutrophil.Elastase.r
3. At the start of the code you will need to load packages required for analysis, for example:

library(vegan)

• If you don't have this package you will need to install it, for example:

install.pakcages("vegan")