cookbook: merge introduction into welcome

Author: Carol-seven

cookbook/_quarto.yml

@@ -9,7 +9,6 @@ book:
   site-url: https://uconn-scs.github.io/msDiaLogue/cookbook/
   chapters:
     - index.qmd
-    - intro.qmd
 
 bibliography: ../inst/REFERENCES.bib
 

cookbook/index.qmd

@@ -9,3 +9,53 @@ mass spectrometry-based proteomics data using **msDiaLogue** in R.
 Each recipe focuses on one module of the analysis workflow, allowing users
 to easily combine recipes into workflows that best fit their own analyses.
 
+
+## What is msDiaLogue?
+
+
+**msDiaLogue** is an R package developed through a collaboration between
+the [Proteomics & Metabolomics Facility (PMF)](https://proteomics.uconn.edu/)
+and the [Statistical Consulting Services (SCS)](https://statsconsulting.uconn.edu/)
+at the [University of Connecticut (UConn)](https://uconn.edu/)
+It provides a modular workflow for analyzing untargeted mass spectrometry
+(MS)-based proteomics data, together with a wide range of visualization options
+for both Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA)
+datasets.
+
+
+::: {style="text-align: center;"}
+[![UConn](https://raw.githubusercontent.com/uconn-scs/msDiaLogue/main/man/figures/uconn.png){style="width:34%; margin:0 2%"}](https://uconn.edu/)
+[![CORE](https://raw.githubusercontent.com/uconn-scs/msDiaLogue/refs/heads/main/man/figures/core.png){style="width:30.6%; margin:0 2%"}](https://core.uconn.edu/)
+[![SCS](https://raw.githubusercontent.com/uconn-scs/msDiaLogue/refs/heads/main/man/figures/scs.png){style="width:25.5%; margin:0 0%"}](https://statsconsulting.uconn.edu/)
+:::
+
+
+## Design philosophy
+
+
+Unlike monolithic analysis pipelines, **msDiaLogue** is designed as a modular
+workflow.
+Each analysis step is implemented as an independent module that can be used on
+its own or combined with other modules.
+This design allows users to adapt the workflow to different experimental designs,
+software platforms, and analysis objectives.
+
+
+## Workflow
+
+
+:::: {style="text-align: center;"}
+![](https://raw.githubusercontent.com/uconn-scs/msDiaLogue/refs/heads/main/man/figures/workflow.png)
+::::
+
+
+## Organization of this cookbook
+
+
+The cookbook is organized into independent recipes corresponding to the major
+modules of **msDiaLogue**.
+Each chapter introduces one module using practical examples and can be read
+independently.
+Readers may follow the recipes in sequence as a complete workflow or use
+individual chapters as references for specific analysis tasks.
+