protGear
Protein Micro Array Data Management and Interactive Visualization
Bioconductor version: Release (3.19)
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("protGear")):
Installation
To install this package, start R (version "4.4") 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")| protGear | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Bayesian, BiomedicalInformatics, Clustering, ImmunoOncology, Microarray, Normalization, OneChannel, Preprocessing, Proteomics, Regression, Software, SystemsBiology |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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) |
| System Requirements | |
| URL | https://github.com/Keniajin/protGear |
| Bug Reports | https://github.com/Keniajin/protGear/issues |
See More
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | protGear_1.8.0.tar.gz |
| Windows Binary (x86_64) | protGear_1.8.0.zip |
| macOS Binary (x86_64) | protGear_1.8.0.tgz |
| macOS Binary (arm64) | protGear_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/protGear |
| Source Repository (Developer Access) | git clone [email protected]:packages/protGear |
| Bioc Package Browser | https://code.bioconductor.org/browse/protGear/ |
| Package Short Url | https://bioconductor.org/packages/protGear/ |
| Package Downloads Report | Download Stats |