BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R

Motivation: We previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration ('BloodGen3' module repertoire) that comprises 382 functionally annotated modules and encompasses 14 168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results: We have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states.

Automated summary

This study introduces an R package, BloodGen3Module, to facilitate group comparison analyses at the module level and display results as annotated fingerprint grid plots. Additionally, it provides a parallel workflow for computing module repertoire changes for individual samples and displays results as fingerprint heatmaps. This resource aims to assist in analyzing and interpreting changes in blood transcript abundance across various pathological and physiological states.