From b7826cbf3678d7ae8aa7a93c20d88bdc81962e4f Mon Sep 17 00:00:00 2001
From: huangyaqing-123 <hyaqing1023@gmail.com>
Date: Fri, 11 Jul 2025 11:21:55 -0400
Subject: [PATCH] Update README

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 README.md | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

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 This is a repository for work with Yaqing Huang.
 
 ## We are focusing on 1-D embeddings of pathway state.
+
+
+# PathwayEmbed
+
+[![Build Status](https://github.com/RaredonLab/PathwayEmbed/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/RaredonLab/PathwayEmbed/actions)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
+
+---
+
+## Installation
+
+You can install the released version of PathwayEmbed from GitHub using:
+
+```r
+# Install remotes if you haven't already
+if (!requireNamespace("remotes", quietly = TRUE)) {
+  install.packages("remotes")
+}
+
+remotes::install_github("RaredonLab/PathwayEmbed")
+
+```r
+---
+
+## Usage
+
+```r
+library(PathwayEmbed)
+
+# Load example data included with the package
+data(fake_test_object)
+
+# Compute pathway data
+mds_results <- ComputeCellData(fake_test_object, pathway = "Wnt", distance.method = "manhattan")
+
+# Prepare data for plotting
+plot_data <- PreparePlotData(fake_test_object, mds_results, group = "genotype")
+
+# Plot pathway activation
+PlotPathway(to.plot = plot_data, pathway = "Wnt", group = "genotype", color = c("#ae282c", "#2066a8"))
+
+# Calculate percentage and do comparison between two groups (optional)
+CalculatePercentage(to.plot = plot_data, group_var = "genotype")
+
+```r