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Welcome to the **msDiaLogue Cookbook**!
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This book provides practical, example-driven recipes for analyzing mass
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spectrometry-based proteomics data using **msDiaLogue** in R.
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Each recipe focuses on one module of the analysis workflow, allowing users can
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easily combine recipes into workflows that best fit their own analyses.
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**msDiaLogue** is an R package developed through a collaboration between
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the [Proteomics & Metabolomics Facility (PMF)](https://proteomics.uconn.edu/)
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and the [Statistical Consulting Services (SCS)](https://statsconsulting.uconn.edu/)
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at the [University of Connecticut (UConn)](https://uconn.edu/)
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It provides a modular workflow for analyzing untargeted mass spectrometry
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(MS)-based proteomics data, together with a wide range of visualization options
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for both Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA)
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datasets.
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::: {style="text-align: center;"}
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[![UConn](https://raw.githubusercontent.com/uconn-scs/msDiaLogue/main/man/figures/uconn.png){style="width:34%; margin:0 2%"}](https://uconn.edu/)
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[![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/)
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[![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/)
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:::
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This book provides practical, example-driven recipes for analyzing
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mass spectrometry-based proteomics data using **msDiaLogue** in R.
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Each recipe focuses on one module of the analysis workflow, allowing users
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to easily combine recipes into workflows that best fit their own analyses.
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