Package: gDR 1.11.23

Arkadiusz Gladki

gDR: Umbrella package for R packages in the gDR suite

Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.

Authors:Allison Vuong [aut], Bartosz Czech [aut], Arkadiusz Gladki [cre, aut], Marc Hafner [aut], Dariusz Scigocki [aut], Janina Smola [aut], Sergiu Mocanu [aut]

gDR_1.11.23.tar.gz
gDR_1.11.23.zip(r-4.7-any)gDR_1.11.23.zip(r-4.6-any)gDR_1.11.23.zip(r-4.5-any)
gDR_1.11.23.tgz(r-4.6-any)gDR_1.11.23.tgz(r-4.5-any)
gDR_1.11.23.tar.gz(r-4.7-any)gDR_1.11.23.tar.gz(r-4.6-any)
gDR_1.11.23.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDR/json (API)

# Install 'gDR' in R:

install.packages('gDR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gdrplatform/gdr/issues

Pkgdown/docs site:https://gdrplatform.github.io

Datasets:

small_combo_data - Small data.table with raw combo data used for processing via gDR
small_data - Small data.table with raw data used for processing via gDR

On BioConductor:gDR-1.11.18(bioc 3.24)gDR-1.10.0(bioc 3.23)

software dataimport shinyapps

6.46 score 2 stars 29 scripts 304 downloads 12 exports 157 dependencies

Last updated from:5bcd71e250. Checks:4 ERROR, 6 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	210
linux-devel	OK	341
source / vignettes	OK	273
linux-release	OK	304
macos-release	OK	158
macos-oldrel	OK	262
windows-devel	ERROR	255
windows-release	ERROR	262
windows-oldrel	ERROR	223
wasm-release	OK	171

Exports:add_treatment_column apply_custom_metadata_tags cast_to_wide convert_growth_metric create_symlink_to_current filter_treatments generate_incucyte_yaml_draft get_next_version_dir import_data label_periods resolve_incucyte_config_path run_report

Dependencies:abind assertthat backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bit bit64 boot broom bslib BumpyMatrix cachem car carData cellranger charport checkmate cli clipr codetools colorspace cowplot cpp11 crayon curl data.table DelayedArray Deriv digest doBy dplyr drc evaluate farver fastmap fontawesome forcats forecast foreign formatR Formula fracdiff fs futile.logger futile.options gDRcore gDRimport gDRutils generics GenomicRanges ggplot2 glue gtable gtools haven highr hms htmltools IRanges isoband jquerylib jsonlite jsonvalidate knitr labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcomp MultiAssayExperiment mvtnorm nlme nloptr nnet numDeriv openxlsx pbkrtest pillar pkgconfig plotrix prettyunits progress purrr qs2 quantreg R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack readr readxl reformulas rematch rio rlang rmarkdown S4Arrays S4Vectors S7 sandwich sass scales Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment survival TH.data tibble tidyr tidyselect timeDate tinytex tzdb urca utf8 V8 vctrs viridisLite vroom whisker withr writexl xfun XML XVector yaml zip zoo

gDR suite

Rendered fromgDR.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2021-03-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add Treatment Column to a Data Table	add_treatment_column
Apply Custom Metadata Tags to Drug Names	apply_custom_metadata_tags
Reshape a data.table from long to wide format	cast_to_wide
Express normalized growth rates in a chosen growth metric	convert_growth_metric
Create symbolic link to current version	create_symlink_to_current
Filter Treatments from SummarizedExperiment	filter_treatments
Generate a Draft YAML Configuration for Incucyte Analysis	generate_incucyte_yaml_draft
Get next version directory	get_next_version_dir
Import raw data	import_data
Display labels for the growth-rate periods of the Incucyte analysis	label_periods
Resolve the configuration file an Incucyte report reads	resolve_incucyte_config_path
Run a gDR report pipeline	run_report
Small data.table with raw combo data used for processing via gDR	small_combo_data
Small data.table with raw data used for processing via gDR	small_data