From 24eba106eb69896acf9e13f10d890fccad8412e1 Mon Sep 17 00:00:00 2001
From: Youness Azimzade <92576728+YounessAzimzade@users.noreply.github.com>
Date: Fri, 17 Jan 2025 18:25:32 +0100
Subject: [PATCH] Update README.md

---
 README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/README.md b/README.md
index 12b082f..07bb553 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,13 @@ This package is under development and not yet available on PyPI. You can, noneth
 pip install git+https://github.com/ocbe-uio/pCRscore.git
 ```
 
+# Expected Input
+
+This package takes cell fractions, likly from spatial proteomics, scRNA seq or estimations using deconvolution methods and clinical out come (pCR vs RD- residual disease). It is possible to provide the cohort alongside these information, otherwise the code randomly assigns the rows to discovery and validation cohorts. 
+
+# Expected Output
+For each cell type, a pCR score is assined and provided in csv file. Ucertanity values for these scores are also provided. 
+
 # References
 
 Explainable Machine Learning Reveals the Role of the Breast Tumor Microenvironment in Neoadjuvant Chemotherapy Outcome