GladiaTOX
This is the development version of GladiaTOX; for the stable release version, see GladiaTOX.
R Package for Processing High Content Screening data
Bioconductor version: Development (3.24)
GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.
Author: Vincenzo Belcastro [aut, cre], Dayne L Filer [aut], Stephane Cano [aut]
Maintainer: PMP S.A. R Support <DL.RSupport at pmi.com>
citation("GladiaTOX")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GladiaTOX")
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("GladiaTOX")| GladiaTOX | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Normalization, Preprocessing, QualityControl, Software, WorkflowStep |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.6.0), data.table (>= 1.9.4) |
| Imports | DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML |
| System Requirements | |
| URL | https://github.com/philipmorrisintl/GladiaTOX |
See More
| Suggests | roxygen2, knitr, rmarkdown, testthat, BiocStyle |
| 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 | GladiaTOX_1.29.0.tar.gz |
| Windows Binary (x86_64) | GladiaTOX_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | GladiaTOX_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | GladiaTOX_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GladiaTOX |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GladiaTOX |
| Bioc Package Browser | https://code.bioconductor.org/browse/GladiaTOX/ |
| Package Short Url | https://bioconductor.org/packages/GladiaTOX/ |
| Package Downloads Report | Download Stats |