protGear
Protein Micro Array Data Management and Interactive Visualization
Bioconductor version: 3.23 · Package version: 1.16.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("protGear")Details
| Maintainer | Kennedy Mwai <keniajin@gmail.com> |
| Author | Kennedy Mwai [cre, aut], James Mburu [aut], Jacqueline Waeni [ctb] |
| License | GPL-3 |
| URL | https://github.com/Keniajin/protGear |
| Bug Reports | https://github.com/Keniajin/protGear/issues |
| Downloads rank | 260 |
| Source branch | RELEASE_3_23 |
| biocViews | BatchEffect, Bayesian, BiomedicalInformatics, Clustering, ImmunoOncology, Microarray, Normalization, OneChannel, Preprocessing, Proteomics, Regression, Software, SystemsBiology |
Documentation
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Dependencies
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)
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)