BZINB-iMMPath

Introduction

Data

• The raw ZOE2.0 Kraken2/Bracken microbiome data is available in the Carolina Digital Repository (https://cdr.lib.unc.edu/concern/data_sets/5d86p890x) in the file CDR_ZOEmicro_20220519.zip > ZOE2_main_Bracken/. The data file used in the scripts in this project was processed by Dr. Hunyong Cho (https://github.com/Hunyong/) using the C01_data.reading.bracken2021.R script from https://github.com/Hunyong/ZOE_metagenomics_2022/tree/main/scripts.
• The ZOE2.0 metabolite data is available in the MetaboLights repository (https://www.ebi.ac.uk/metabolights/MTBLS2215/files).

Software

• To install the BZINB package, please run the following line: install_github("Hunyong/BZINB")

Description of scripts

• process_data.R Filter and save data in R lists of data frames for further analysis
• simulation_lognormal.R Simulate pairs of vectors from the bivariate lognormal distribution and calculate correlations (figure 5) - 10 replicates as an example.
• simulation_bzinb.R simulate pairs of vectors from the BZINB distribution and calculate correlations (figure 6) - 10 replicates as an example.
• fit_example.R code to fit the BZINB model on and calculate correlation for pairs of count vectors - 10 pairs at a time.
• spectral.m matlab code for spectral clustering based on affinity matrix using non-negative correlations. The spectral clustering and asymmetrical clustering packages can be downloaded at https://sites.stat.washington.edu/mmp/software.html (http://www.stat.washington.edu/spectral/code/SpectraLib.tgz and http://www.stat.washington.edu/spectral/code/SpectraLib_A.tar).