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 (3.17)

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>

Citation (from within R, enter citation("protGear")):

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 1.3.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 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), kableExtra (>= 1.3.4), 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
macOS Binary (x86_64) protGear_1.3.0.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
Package Short Url https://bioconductor.org/packages/protGear/
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