Input and output files of the case studies included in the manuscript "MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration".

This repository contains the input and output files necessary to reproduce the case studies reported in the manuscript "MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration". MUUMI is an R package implementing network-based data integration and statistical meta-analysis within a single analytical framework. MUUMI allows the identification of robust molecular signatures through multiple meta-analytic methods, inference and analysis of molecular interactomes and the integration of multiple omics layers. The functionalities of MUUMI are showcased in two case studies in which we analysed 17 transcriptomic datasets on idiopathic pulmonary fibrosis (IPF) from both microarray and RNA-Seq platforms and multi-omics data of THP-1 macrophages exposed to different polarising stimuli. Part of the data reported in this repository derive from the Zenodo entry https://doi.org/10.5281/zenodo.10692129 (Curated and harmonised transcriptomics datasets of interstitial lung disease patients). Other data derive from the following publication: Migliaccio G, Morikka J, del Giudice G, Vaani M, Möbus L, Serra A, Federico A, Greco D. Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages, Comp and Struct Biotech J, 2024(25), 143-152. doi: 10.1016/j.csbj.2024.08.018.