ibiomic

sample-to-sample comparisons 

2 groups of samples: differential expression analysis

gene ontology for the obtained gene lists

visualization and reporting: sample-to-sample scatterplots, similarity indexes, volcano plots, box plots/violin plots for important groups of genes

differential expression analysis between sample groups

gene ontology for the obtained gene lists

quality control by calculating similarity index

visualization and reporting: volcano plots, box plots/violin plots for important groups of genes, sample-to-sample scatterplots, tables of significant gene lists and corresponding gene ontology terms, similarity index tables,  samples-outliers are emphasized in separate plots if found.

differential expression genes between groups of samples

gene ontology for the obtained gene lists

representation of samples in low-dimensional space

visualization and reporting: tables of significant gene lists and corresponding gene ontology terms, box plots/violin plots for important groups of genes, reduced-dimensionality scatterplots with samples represented as points,  volcano plots provided only if needed. 

cells clustering and identification

differential expression

gene ontology

visualization and reporting: tables of significant gene lists, tables of gene clusters and cells, heatmaps, box plots/violin plots for important groups of genes, reduced-dimensionality scatterplots (tSNE).

multivariate biomarker search: in some cases a few genes or proteins are enough to clearly distinguish between groups of samples. In case of disease vs control group this indicates availability of diagnostic biomarker for the disease. This analysis is recommended for human blood proteomics.

visualization and reporting: tables of most indicative genes/proteins with formulas/rules how biomarker is created, box plots/violin plots for obtained multivariate biomarker(s), basic analysis of gene/protein list.

clusters of highly correlated genes

gene ontology for the obtained gene lists

differential expression and similarity index are provided if reasonable for specific dataset

representation of samples in low-dimensional scatterplots with trajectories

visualization and reporting: tables of significant gene lists and corresponding gene ontology terms, time-series plots, box plots/violin plots for important groups of genes, gene-to-gene scatterplots with samples represented as points, with and without trajectories.