https://github.com/keniajin/protgear
protGear is a package for protein microarray data processing just before the main analysis.
https://github.com/keniajin/protgear
background-correction microarray-data normalisation proteomics-data r shiny shinydashboard
Last synced: 11 months ago
JSON representation
protGear is a package for protein microarray data processing just before the main analysis.
- Host: GitHub
- URL: https://github.com/keniajin/protgear
- Owner: Keniajin
- Created: 2020-12-11T11:20:58.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2023-02-03T19:25:58.000Z (about 3 years ago)
- Last Synced: 2024-04-26T20:49:39.796Z (almost 2 years ago)
- Topics: background-correction, microarray-data, normalisation, proteomics-data, r, shiny, shinydashboard
- Language: R
- Homepage: https://keniajin.github.io/protGear/
- Size: 41.9 MB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## 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