HDXBoxeR is a tool designed to streamline various aspects of HDX
(Hydrogen-Deuterium Exchange) data analysis:
Data Reprocessing: Reprocesses data to the format
required for data publication.
Parameter Calculation: Calculates parameters for a
general HDX summary table, including backexchange, peptide lengths, and
statistical information.
Output Conversion: Converts output from HDXExaminer
(formerly Sierra Analytics, now Trajan Scientific) to a more manageable
and analyzable format.
Statistical Analysis: Identifies peptides
significantly different between sets using Welch T-tests.
Script Generation: Generates scripts for Pymol
visualization.
Plot Generation: Facilitates easy plot generation,
including heat maps, robot plots (modified butterfly plots), significant
peptides, volcano plots, and average deuteration.
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:
CRAN
To install, use the following command:
install.packages(“HDXBoxeR”) #execute only once
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
After installing HDXBoxeR in R, load the package using following
command: