MEP_r scripts

R package(s) for reproducibility and efficiency of microbiome analyses.

Motivation

To simplify analysis of REDCap exports for metadata analyses and summaries, statistical analysis, and vizualization, our most commonly used R functions from the MEP are stored in this repo.

Description by function

• get_prefix: provided a list of sample names, a delimiter, and option to include human microbiome project (HMP) standard prefix of SRS, a list of unique prefixes is produced that can be used for analysis by prefix.

• bracken_clean: provided the output tables from the combine output script from bracken, clean based on minimum abundance, sample names, and taxonomic names.

Installation

1. Install devtools:

install.packages("devtools")

2. Load devtools:

library(devtools)

3. Install MEP_r package:

install_github("michaelwoodworth/MEP_r")