Cirrhosis data

Data were originally published by Qin et al., 2014 (DOI: 10.1038/nature13568) and were downloaded from the ML repo (https://github.com/knights-lab/MLRepo, accessed on 27/01/2021). The data set consists of 130 stool samples from cirrhotic and healthy individuals, from which Qin et al. extracted gDNA and sequenced it via an Illumina HiSeq sequencer. They profiled metagenomes with BURST and Prokaryotic RefSeq Genomes. The downloaded taxonomic profiles consisted of read counts for taxonomic levels not collapsed at coarser level (i.e., if a read count had been assigned to the species level, the number of count of the genus was not indicated). Consequently, we calculated the read counts for each taxonomic level by summing read counts of all species in the clade. Relative abundances were then normalized per the total number of reads to obtain relative abundances. Taxa were filtered using a progressive threshold as described in our paper (https://www.biorxiv.org/content/10.1101/2022.01.03.474763v1). ------------------------------------------------------ Cirrhosis_X: relative abundances of human gut microbiome of individuals with/without cirrhosis Cirrhosis_y: labeling of healthy and cirrhosis individuals