README.md

In quangnguyen1995/micrec: Tidy recipes for microbiome data analysis

micrec: Tidy recipes for microbiome data analysis

Overview

Work in progress! This package is a wrapper around popular microbiome methods implemented packages such as phyloseq or vegan in the context of parsnip, recipe and workflows in the tidymodels ecosystem. Specifically, tidymodels allow for a unified tidy approach to data transformation, modelling and evaluation. It is also a way to keep provenance of analysis objects for reproducibility and sharing across researchers without having to slog through tons of code. A practitioner can print a recipe model and examine data preprocessing steps, which is vital in microbiome data analysis. The desire to have a separate package to support phyloseq objects is also because operations done on taxonomic data, such as tip_glom or tax_glom affect multiple layers of data, such as the phylogenetic tree, taxonomic table, etc. This is not readily available in vanilla recipes This small package takes advantage of the readily available tools in parsnip and recipe to import custom methods in order to create a suite of step_ functions and parsnip engines specific to microbiome research that can readily be used in the tidymodels context. The long term goal is to evolve around the tidymodels ecosystem, with the really far-fetched goal of also support ExpressionSet type objects in Bioconductor.

Installation

Install this work in progress using devtools/remotes package

remotes::install_github('quangnguyen1995/micrec') 

quangnguyen1995/micrec documentation built on March 2, 2020, 12:12 a.m.