Helper functions to run the dada2 pipeline on nemabiome data. This package provides some convience functions for running an analysis with dada2. Primarily designed for analyzing nemabiome data but can be used for other dada2 analysis. Includes a script to run the analysis.
You can install nemabiomeR from Github with:
devtools::install_github("ucvm/nemabiomeR")Cutadapt is required to use clip_primers function. The recommended way to install cutadapt is from bioconda.
Install the package to get access to the helper functions. You can then download the run_pipeline.R script as a place to start your analysis.