protGear

DOI: 10.18129/B9.bioc.protGear  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see protGear.

Protein Micro Array Data Management and Interactive Visualization

Bioconductor version: 3.17

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Author: Kennedy Mwai [cre, aut], James Mburu [aut], Jacqueline Waeni [ctb]

Maintainer: Kennedy Mwai <keniajin at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("protGear")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("protGear")

 

HTML	R Script	protGear
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Bayesian, BiomedicalInformatics, Clustering, ImmunoOncology, Microarray, Normalization, OneChannel, Preprocessing, Proteomics, Regression, Software, SystemsBiology
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.2), dplyr (>= 0.8.0), limma(>= 3.40.2), vsn(>= 3.54.0)
Imports	magrittr (>= 1.5), stats (>= 3.6), ggplot2 (>= 3.3.0), tidyr (>= 1.1.3), data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2), tibble (>= 3.1.0), rmarkdown (>= 2.9), knitr (>= 1.33), utils (>= 3.6), genefilter(>= 1.74.0), readr (>= 2.0.1), Biobase(>= 2.52.0), plyr (>= 1.8.6), Kendall (>= 2.2), shiny (>= 1.0.0), purrr (>= 0.3.4), plotly (>= 4.9.0), MASS (>= 7.3), htmltools (>= 0.4.0), flexdashboard (>= 0.5.2), shinydashboard (>= 0.7.1), GGally (>= 2.1.2), pheatmap (>= 1.0.12), grid (>= 4.1.1), styler (>= 1.6.1), factoextra (>= 1.0.7), FactoMineR (>= 2.4), rlang (>= 0.4.11), remotes (>= 2.4.0)
LinkingTo
Suggests	gridExtra (>= 2.3), png (>= 0.1-7), magick (>= 2.7.3), ggplotify (>= 0.1.0), scales (>= 1.1.1), shinythemes (>= 1.2.0), shinyjs (>= 2.0.0), shinyWidgets (>= 0.6.2), shinycssloaders (>= 1.0.0), shinyalert (>= 3.0.0), shinyFiles (>= 0.9.1), shinyFeedback (>= 0.3.0)
SystemRequirements
Enhances
URL	https://github.com/Keniajin/protGear
BugReports	https://github.com/Keniajin/protGear/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	protGear_1.4.0.tar.gz
Windows Binary	protGear_1.4.0.zip
macOS Binary (x86_64)	protGear_1.4.0.tgz
macOS Binary (arm64)	protGear_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/protGear
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/protGear
Bioc Package Browser	https://code.bioconductor.org/browse/protGear/
Package Short Url	https://bioconductor.org/packages/protGear/
Package Downloads Report	Download Stats