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protGear
This is thedevelopment version of protGear; for the stable release version, seeprotGear.
Protein Micro Array Data Management and Interactive Visualization
Bioconductor version: Development (3.23)
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("protGear")For older versions of R, please refer to the appropriateBioconductor 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 | 1.15.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | protGear_1.15.0.tar.gz |
| Windows Binary (x86_64) | protGear_1.15.0.zip (64-bit only) |
| macOS Binary (x86_64) | protGear_1.15.0.tgz |
| macOS Binary (arm64) | protGear_1.15.0.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 |