Autism_SupplementaryMaterial

This repository contains supplementary materials relating to the manuscript "Untargeted metabolomic study of autism in newborn screening samples: a pilot study" by J. Courraud (@Althalis), M. Ernst (@madeleineernst), S.S. Laursen, D. M. Hougaard, A.S. Cohen.

KendrickMassFilter

This folder contains the Jupyter notebooks adapted from da Silva and collaborators (2019) used to filter our data for undesired chemical background of repeat units typical of polyethylene glycol (PEG) and polypropylene glycol (PPG) through a Kendrick Mass Filter.

PCoA

This folder contains the Jupyter notebook used to create the interactive principal coordinates analysis (PCoA) plots using the Bray-Curtis, Canberra, Jaccard and Robust Aitchison dissimilarities within Qiime2 and EMPeror.

PERMANOVA

This folder contains the Jupyter notebook used to perform the Permutational Multivariate Analysis of Variance (PERMANOVA) to assess the variation in the metabolome explained by collected metadata.

Citation

Courraud J, Ernst M, Laursen SS, Hougaard DM, Cohen AS. Untargeted metabolomic study of autism in newborn screening samples: a pilot study. 2020; medRxiv.

da Silva RR, Vargas F, Ernst M et al. Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter. J Am Soc Mass Spectrom 2019; 30: 268-277.

Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37: 852-857.

Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. EMPeror: a tool for visualizing high-throughput microbial community data. GigaScience 2013; 16.