useR! 2024

Make-it-easy-pipeline (MIEP) is an integrated, interactive, user-friendly pipeline for RNA-seq data. This new R package helps researchers develop testable hypotheses and select targets for wet lab functional testing. MIEP performs statistical testing, annotates sequences, corrects biases, and summarizes results in HTML tables, volcano plots, and heat maps. Shiny apps allow to modify default settings, select a data shrinkage method, and set thresholds to identify differentially expressed features. Use of MIEP in a cancer research project facilitated the identification of phenotype-linked signal transduction pathways whose biological relevance was experimentally verified. MIEP’s functions include: - Dimensionality reduction and visualizations by PCA, UMAP, tSNE, SVM - Enrichment of Gene Ontology (GO) terms - Calculation of features’ importance subsequent to classification (conditional random forests) - Gene set editing based on the ranking of GO terms or features’ importance - Analyses focused on gene sets and user-friendly graphical representations. These characteristics and careful handling of exceptions make MIEP an easy-to-use tool for biologists with basic programming skills.