Introduction

The AllInOne is an open-Source, R-Shiny user interface package designed in the Plant Agriculture department at the University of Guelph to provide a broad range of pre-processing analysis features for phenotypic datasets.

Pre-processing steps in AllInone can be summarized as:

Changing the structure of the dataset
Detecting missing patterns in the dataset
Imputing missing data using different statistical methods
Data visualization in order to check data patterns and distribution
Detecting and refining outliers using quantile and/or cook’s distance methods
Estimating correlations among dependent variables and with and within independent variables
Normalizing data based on the optimum normalization methods for a given dataset
Estimating heritability and conducting spatial analysis
Calculating the best linear unbiased prediction (BLUP) or/and best linear unbiased estimator (BLUE)
Enabling plant scientists to use different packages simultaneously in an interactive environment
Allowing plant scientists to edit, organize, subset, and sort datasets in a live mode