gDRimport
This is the released version of gDRimport; for the devel version, see gDRimport.
Package for handling the import of dose-response data
Bioconductor version: Release (3.23)
The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.
Author: Arkadiusz Gladki [aut, cre]
, Bartosz Czech [aut]
, Marc Hafner [aut]
, Sergiu Mocanu [aut], Dariusz Scigocki [aut], Allison Vuong [aut], Luca Gerosa [aut]
, Janina Smola [aut]
Maintainer: Arkadiusz Gladki <gladki.arkadiusz at gmail.com>
citation("gDRimport")):
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")
BiocManager::install("gDRimport")
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("gDRimport")| Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet | HTML | R Script |
| Converting PharmacoSet Drug Response Data into gDR object | HTML | R Script |
| gDRimport | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2) |
| Imports | assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx, data.table, futile.logger, gDRutils(>= 1.7.1), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx, qs2 |
| System Requirements | |
| URL | https://github.com/gdrplatform/gDRimport https://gdrplatform.github.io/gDRimport/ |
| Bug Reports | https://github.com/gdrplatform/gDRimport/issues |
See More
| Suggests | BiocStyle, gDRtestData(>= 1.7.1), gDRstyle(>= 1.7.1), knitr, purrr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | gDR |
| Imports Me | |
| Suggests Me | gDRcore |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gDRimport_1.10.0.tar.gz |
| Windows Binary (x86_64) | gDRimport_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | gDRimport_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | gDRimport_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gDRimport |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gDRimport |
| Bioc Package Browser | https://code.bioconductor.org/browse/gDRimport/ |
| Package Short Url | https://bioconductor.org/packages/gDRimport/ |
| Package Downloads Report | Download Stats |