Microbiome co-occurence networks constructed from a total of 4143 samples from 32 studies and 10 phenotypic states including: Healthy, advanced (colorectal) adenomas (AA), atherosclerotic cardiovascular disease (ACVD), colorectal cancer (CRC), Crohn's disease (CD), obesity (OB), overweight (OW), rheumatoid arthritis (RA), Type-2 diabetes (T2D), ulcerative colitis (UC).
Script used to preprocess sra files into respective network GML files.
- generate_cooccurrence_network.sh
Graph_files
- *.csv - CSV file of individual node annotations
- *.gml - GML file of generated co-occurrence networks
Supplementary_Files
- Supplementary_Table_1.csv - Metadata of accession numbers used in this analysis
data
- bracken.biom.tar.gz - bracken abundance matrix of all samples
- seq_depth.log - log of sequencing depth of pre- and post-filtered fastq files
lib
- scripts used in this analysis