General information

protGear is a package for protein micro-array data processing just before the main analysis.

The package loads the 'gpr' or 'txt' file format extracted by the quantification software and merges this with the specific sample identifiers. The package processes multiple files extracted in a batch with their corresponding sample identifier file. The sample identifier file has 2 variables 'v1' and 'v2' which indicate the mini-array or block number and sample identifier respectively. The 'gpr' file and the corresponding sample identifier file have the same file name. protGear also provides a web based $Shiny^{(R)}$ platform for real time visualization of the data processing.

There is a package vignette included with this package with a step by step use of the package. Check https://keniajin.github.io/protGear/ under articles.

Installing the devel package

library(remotes) 
remotes::install_github("keniajin/protGear")

Installing from Bioc BioConductor

## install from BioConductor
if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("protGear")

To run the shiny application

To use the application locally on your compute install R and launch the app using the following command. protGear::launch_protGear_interactive()

To Install R:

• Open an Internet browser and go to www.r-project.org.
• Under "Getting Started" click the "download R" link
• Select a CRAN location (a mirror site) and click the corresponding link.
• Download R depending on your operating system.

protGear help pages

• The main page - https://keniajin.github.io/protGear/
• Vignette - https://keniajin.github.io/protGear/articles/vignette.html

Contribute

Check the Github page for source code.

Publication

Mwai K, Kibinge N, Tuju J, Kamuyu G, Kimathi R, Mburu J, Chepsat E, Nyamako L, Chege T, Nkumama I, Kinyanjui S. et al. , protGear: A protein microarray data pre-processing suite. Computational and Structural Biotechnology Journal. 2021 Apr 24.

DOI: https://doi.org/10.1016/j.csbj.2021.04.044