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.
HDXBoxeR can be used to enhance the efficiency and effectiveness of HDX data analysis, providing tools for data processing, analysis, and visualization.
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:
To install, use the following command:
install.packages("HDXBoxeR") #execute only once
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")
After installing HDXBoxeR in R, load the package using following command:
library(HDXBoxeR)
Please access the vignette with examples at:
https://cran.r-project.org/web//packages/HDXBoxeR/vignettes/HDXBoxeR.html
After HDXBoxeR package installation the test data will be located in system files of the HDXBoxeR. The path to the input table is shown below:
file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
This project is licensed under the GPL (>= 2) licence