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 (3.23)
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 (from within R, enter 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 devel
BiocManager::install(version='devel')
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")
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
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
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Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/protGear
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/protGear