## 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 ``` r library(remotes) remotes::install_github("keniajin/protGear") ``` ## Installing from Bioc BioConductor ``` r ## 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](https://github.com/Keniajin/protGear/). ## 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