Package: gDRimport 1.11.13

Arkadiusz Gladki

gDRimport: Package for handling the import of dose-response data

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.

Authors: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]

gDRimport_1.11.13.tar.gz
gDRimport_1.11.13.zip(r-4.7-any)gDRimport_1.11.13.zip(r-4.6-any)gDRimport_1.11.13.zip(r-4.5-any)
gDRimport_1.11.13.tgz(r-4.6-any)gDRimport_1.11.13.tgz(r-4.5-any)
gDRimport_1.11.13.tar.gz(r-4.7-any)gDRimport_1.11.13.tar.gz(r-4.6-any)
gDRimport_1.11.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDRimport/json (API)

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

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

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

On BioConductor:gDRimport-1.11.12(bioc 3.24)gDRimport-1.10.0(bioc 3.23)

softwareinfrastructuredataimport

7.93 score 3 stars 1 packages 27 scripts 400 downloads 29 exports 133 dependencies

Last updated from:4ec3d8c256. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING207
linux-develOK335
source / vignettesOK449
linux-releaseOK372
macos-releaseOK282
macos-oldrelOK169
windows-develOK204
windows-releaseOK293
windows-oldrelOK299
wasm-releaseOK201

Exports:check_metadata_namesconvert_LEVEL5_prism_to_gDR_inputconvert_LEVEL6_prism_to_gDR_inputconvert_MAE_to_PSetconvert_pset_to_dfdetect_file_formatget_exception_dataget_import_provenanceget_test_D300_dataget_test_dataget_test_EnVision_dataget_test_Tecan_dataget_test_tsv_datagetPSetimport_D300is_readable_vload_dataload_long_tableload_manifestload_resultsload_templatesmanifest_pathparse_D300_xmlread_excel_to_dtresult_pathsetEnvForPSetstandardize_record_valuestemplate_pathvalidate_gdr_input

Dependencies:abindassertthatbackportsBiobaseBiocBaseUtilsBiocGenericsbitbit64bootbroomBumpyMatrixcarcarDatacellrangercheckmateclicliprcodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArrayDerivdigestdoBydplyrdrcfarverforcatsforecastforeignformatRFormulafracdifffutile.loggerfutile.optionsgDRutilsgenericsGenomicRangesggplot2gluegtablegtoolshavenhmsIRangesisobandjsonlitejsonvalidatelabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrmultcompMultiAssayExperimentmvtnormnlmenloptrnnetnumDerivopenxlsxpbkrtestpillarpkgconfigplotrixprettyunitsprogresspurrrqs2quantregR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreadrreadxlreformulasrematchriorlangS4ArraysS4VectorsS7sandwichscalesSeqinfoSparseArraySparseMstringfishstringistringrSummarizedExperimentsurvivalTH.datatibbletidyrtidyselecttimeDatetzdburcautf8V8vctrsviridisLitevroomwithrwritexlXMLXVectoryamlzipzoo

gDRimport
Overview | Use Cases | Test Data | Load data | Validate input data | PRISM | Processing LEVEL5 PRISM Data | Processing LEVEL6 PRISM Data | Package installation | SessionInfo
Rendered fromgDRimport.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2023-03-29

Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet
Introduction | Loading the gDR-generated MAE object | Converting the MAE object into a PharmacoSet object | TreatmentResponseExperiment Object | Row and Column Names | data.table Subsetting | assays | References
Rendered fromConvertingMAEtoPharmacoSet.Rmdusingknitr::rmarkdown

Last update: 2026-10-02
Started: 2023-10-02

Converting PharmacoSet Drug Response Data into gDR object
Overview | Loading a PharmacoSet (PSet) | Converting PharmacoSet to data.table for gDR pipeline | Subsetting to extract relevant information | Running drug response pipeline with data | SessionInfo
Rendered fromConvertingPharmacoSetToGDR.Rmdusingknitr::rmarkdown

Last update: 2026-10-02
Started: 2023-06-02

Readme and manuals

Help Manual

Help pageTopics
check_metadata_namescheck_metadata_names
Load, convert and process the level 5 PRISM data into a gDR inputconvert_LEVEL5_prism_to_gDR_input
Load, convert and process the level 6 PRISM data into a gDR inputconvert_LEVEL6_prism_to_gDR_input
Convert MultiAssayExperiment to TreatmentResponseExperimentconvert_MAE_to_PSet
Convert a PharmacoSet to a data.table that is prepare for input into gDR pipelineconvert_pset_to_df
Detect format of results datadetect_file_format
Fix typos using reference datafix_typos_with_reference
gDR Test Data objectgdr_test_data-class
Get final results (as a data.table) from raw edited EnVision data.tableget_df_from_raw_edited_EnVision_df
Get final results (as a data.table) from raw unedited EnVision data.tableget_df_from_raw_unedited_EnVision_df
get exception dataget_exception_data
Get names of the sheets expected in templates xlsxget_expected_template_sheets
Where gDR input data came fromget_import_provenance
get test D300 dataget_test_D300_data
get primary test dataget_test_data
get test EnVision dataget_test_EnVision_data
get test Tecan dataget_test_Tecan_data
get test tsv dataget_test_tsv_data
Get PharmacoSetgetPSet
Import D300import_D300
is_readable_v Check if all paths in vector are readableis_readable_v
Load dataload_data
Load long tableload_long_table
Load manifestload_manifest
Load resultsload_results
Load EnVision results from xlsxload_results_EnVision
Load incucyte results from plain textload_results_Incucyte
Load tecan results from xlsxload_results_Tecan
Load results from tsvload_results_tsv
Load templatesload_templates
Load templates from tsvload_templates_tsv
Load templates from xlsxload_templates_xlsx
Parse D300parse_D300_xml
Read excel file and transorm it into data.table objectread_excel_to_dt
for each drug create a Gnumber and Concentration information for each wellsave_drug_info_per_well
Adjust environment variables to meet gDR standardssetEnvForPSet
standardize_record_valuesstandardize_record_values
Validate gDR input data before importprint.gdr_validation validate_gdr_input