Bioinformatics (Oxford, England). 2022-10-14; 38.20: 4735-4744.

FastMix: a versatile data integration pipeline for cell type-specific biomarker inference

Zhang Y, Sun H, Mandava A, Aevermann BD, Kollmann TR, Scheuermann RH, Qiu X, Qian Y

PMID: 36018232


Flow cytometry (FCM) and transcription profiling are the two widely used assays in translational immunology research. However, there is no data integration pipeline for analyzing these two types of assays together with experiment variables for biomarker inference. Current FCM data analysis mainly relies on subjective manual gating analysis, which is difficult to be directly integrated with other automated computational methods. Existing deconvolutional analysis of bulk transcriptomics relies on predefined marker genes in the transcriptomics data, which are unavailable for novel cell types and does not utilize the FCM data that provide canonical phenotypic definitions of the cell types.