protGear

DOI: 10.18129/B9.bioc.protGear  

This is the development version of protGear; for the stable release version, see protGear.

Protein Micro Array Data Management and Interactive Visualization

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("protGear")

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

Documentation

PDF		Reference Manual

Details

biocViews	BatchEffect, Bayesian, BiomedicalInformatics, Clustering, ImmunoOncology, Microarray, Normalization, OneChannel, Preprocessing, Proteomics, Regression, Software, SystemsBiology
Version	1.5.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
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
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Build Report

Package Archives

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

Source Package
Windows Binary	protGear_1.5.0.zip
macOS Binary (x86_64)	protGear_1.5.0.tgz
macOS Binary (arm64)
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