Package: gDRtestData 1.11.12

Arkadiusz Gladki

gDRtestData: gDRtestData - R data package with testing dose response data

R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs2 files with MAE data processed by gDR.

Authors:Aleksander Chlebowski [aut], Bartosz Czech [aut], Arkadiusz Gladki [cre, aut], Marc Hafner [aut], Marcin Kamianowski [aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz Scigocki [aut], Janina Smola [aut], Allison Voung [aut]

gDRtestData_1.11.12.tar.gz
gDRtestData_1.11.12.tar.gz(r-4.7-any)gDRtestData_1.11.12.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDRtestData/json (API)

# Install 'gDRtestData' in R:
install.packages('gDRtestData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On BioConductor:gDRtestData-1.11.10(data/experiment 3.24)gDRtestData-1.10.0(data/experiment 3.23)

experimentdatatechnologydatadatapkg

6.70 score 2 stars 15 scripts 14 exports 3 dependencies

Last updated from:be2717ab23. Checks:1 WARNING, 3 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING139
linux-develOK268
source / vignettesOK362
linux-releaseOK287

Exports:add_concentrationadd_data_replicatesadd_day0_datacreate_synthetic_cell_linescreate_synthetic_drugsgenerate_e_infgenerate_ec50generate_hill_coefgenerate_response_dataget_test_dataset_pathsprepareCodilutionDataprepareComboMergedDataprepareDataprepareMergedData

Dependencies:backportscheckmatedata.table

gDRtestData
Overview | Use Cases | Synthetic data generation | Synthetic object of gDR data model | Annotation data | Other | SessionInfo
Rendered fromgDRtestData.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2023-03-28

DepMap Portal Data
Introduction | Data Source & Citation | Data Overview | Data Dictionary | Models (Cell Line Metadata) | Somatic Mutations (Hotspot) | Somatic Mutations (Damaging) | CRISPR Gene Effect | Gene Expression | Copy Number Variation (CNV) | Important Limitations & Disclaimers | SessionInfo
Rendered fromDepMap_Portal_Data.Rmdusingknitr::rmarkdown

Last update: 2026-06-10
Started: 2026-06-01

Readme and manuals

Help Manual

Help pageTopics
Add concentrationsadd_concentration
Add data replicatesadd_data_replicates
Add data with day 0add_day0_data
Create data.table with synthetic cell linescreate_synthetic_cell_lines
Create data.table with synthetic drugscreate_synthetic_drugs
CRISPR Gene Effect ScoresDepMap_CRISPRGeneEffect
DepMap Models (Cell Line Metadata)DepMap_Model
Copy Number Variation (CNV)DepMap_OmicsCNGene
Gene Expression (Log2 TPM)DepMap_OmicsExpressionProteinCodingGenesTPMLogp1
Somatic Mutations (Damaging)DepMap_OmicsSomaticMutationsMatrixDamaging
Somatic Mutations (Hotspot)DepMap_OmicsSomaticMutationsMatrixHotspot
Calculate E inf metricgenerate_e_inf
Calculate EC50 metricgenerate_ec50
Generate hill coefficientgenerate_hill_coef
Generate response datagenerate_response_data
get_test_dataset_pathsget_test_dataset_paths
prepareCodilutionDataprepareCodilutionData
prepareComboMergedDataprepareComboMergedData
prepareDataprepareData
prepareMergedDataprepareMergedData
PRISM Broad Screen Cancer Cell Line Viability DatasetPRISMBroadScreen_Hagenbeek_NatComm_2026