From 094f17a5a7e89ba4d0236ced38ace502a5fced09 Mon Sep 17 00:00:00 2001 From: YiChen Zhu Date: Mon, 23 Feb 2026 22:39:34 -0500 Subject: [PATCH] Updated README with more detailed project description --- README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index bbe9cb3..ce904da 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,12 @@ # Metabolic pathway analysis for Reactome pathways -**Input:** High-throughput metabolite levels for condition and control samples +**Overview:** +MPA is an R package and application that identifies perturbed metabolic pathways from high-throughput metabolite data. It leverages pathway information from the Reactome database to score and rank pathways based on how disrupted they are under experimental conditions. -**Output:** Ranked list of Reactome pathways that perturbed in the condition under study – the rank is based on a score or p-value that results from evaluating the pathway disruption given the data and the pathway information from the Reactome database +### How It Works + +1. **Input:** High-throughput metabolite levels for condition and control samples + +2. **Score computation:** For each pathway, individual reaction perturbation scores are calculated using log₂ fold-change of condition vs. control metabolite levels. These are aggregated into an overall pathway perturbation score. + +3. **Output:** Ranked list of Reactome pathways that perturbed in the condition under study – the rank is based on a score or p-value that results from evaluating the pathway disruption given the data and the pathway information from the Reactome database