Metagenomics Data Analysis
Our metagenomics analysis pipeline reveals the abundance and diversity of microbes at the genus and species level, and maps correlations between different species/populations
We provide a detailed analysis of 16srRNA and 18srRNA, ITS and shotgun metagenome data. This analysis aids in the understanding of the interactions between microbes and their hosts, identification of active pathways, discovery of how microbial gene expression impacts host disease onset and progress, among others| ANALYSIS | SPECIFIC ANALYSIS | OUTPUT |
| Visual Exploration | Abundance Profiling | Stacked bar / area plot, Interactive pie chart, Rarefaction curves, Phylogenetic tree, Heat tree analysis, FB Ratio |
| Microbial community profiling | Alpha Diversity Analysis | Chao 1 Index, ACE, Shannon, Simpson, & Fisher indices |
| T-test/ANOVA p-value & T-statistic, Mann-Whitney/Kruskal-Wallis p-value & Mann-Whitney statistic | ||
| Beta Diversity Analysis | PCOA plot, PERMANOVA, ANOSIM, & PERMDISP statistics | |
| Core Microbiome Analysis | Heatmap and Results Table | |
| Clustering & Correlation | Heatmap Clustering | Hierarchical Clustering & Heatmap Visualization |
| Dendrogram Analysis | Tree based on unweighted Unifrac distance | |
| Correlation Analysis | SparCC correlation tables, network, and boxplots | |
| Comparison and Classification | Classical univariate analysis | T-test/ANOVA p-value & T-statistic, Mann-Whitney/Kruskal-Wallis p-value & Mann-Whitney statistic |
| MetagenomeSeq | Zero inflated Gaussian fit: p-values and FDR values | |
| Differential Abundance Analysis | log2FC, logCPM, P-values, and FDR values | |
| LEfSe Analysis | LDA scores, p-values, FDR values, analysis results table | |
| Random Forest Analysis | MDA Accuracy, OOB error rates, RF plots, important features |
