Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data.

HDXBoxeR

HDXBoxeR is a tool designed to streamline various aspects of HDX (Hydrogen-Deuterium Exchange) data analysis:

1. Data Reprocessing: Reprocesses data to the format required for data publication.
2. Parameter Calculation: Calculates parameters for a general HDX summary table, including backexchange, peptide lengths, and statistical information.
3. Output Conversion: Converts output from HDXExaminer (formerly Sierra Analytics, now Trajan Scientific) to a more manageable and analyzable format.
4. Statistical Analysis: Identifies peptides significantly different between sets using Welch T-tests.
5. Script Generation: Generates scripts for Pymol visualization.
6. Plot Generation: Facilitates easy plot generation, including heat maps, robot plots (modified butterfly plots), significant peptides, volcano plots, and average deuteration.
7. ExtReme Inputs: Generates inputs for ExtReme, enabling comparison between different protein states and discrimination of significantly different peptides.

Usage

HDXBoxeR can be used to enhance the efficiency and effectiveness of HDX data analysis, providing tools for data processing, analysis, and visualization.

Installation & Loading

First, ensure that you have R (and RStudio) installed on your computer. Then you can proceed with the installation of the HDXBoxeR package. There are two methods to install the HDXBoxeR package:

1. CRAN

   To install, use the following command:

install.packages("HDXBoxeR") #execute only once

2. GitHub

   The HDXBoxeR package is available on GitHub and can be installed using the devtools package. This method of installation is an alternative to the CRAN method.

install.packages("devtools") #if not installed library(devtools) #run next two commends only once devtools::install_github("mkajano/HDXBoxeR")

Loading

library(HDXBoxeR)

License

This project is licensed under the GPL (>= 2) licence.