Package: gDRimport 1.10.0

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_1.10.0.tar.gz
gDRimport_1.10.0.zip(r-4.7)gDRimport_1.10.0.zip(r-4.6)gDRimport_1.10.0.zip(r-4.5)
gDRimport_1.10.0.tgz(r-4.6-any)gDRimport_1.10.0.tgz(r-4.5-any)
gDRimport_1.10.0.tar.gz(r-4.7-any)gDRimport_1.10.0.tar.gz(r-4.6-any)
gDRimport_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gDRimport/json (API)
NEWS

# Install 'gDRimport' in R:
install.packages('gDRimport', repos = c('https://bioc-release.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-1.11.2(bioc 3.24)gDRimport-1.10.0(bioc 3.23)

softwareinfrastructuredataimport

7.32 score 3 stars 1 packages 9 scripts 323 downloads 26 exports 203 dependencies

Last updated from:4c07ceeeea (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE219
linux-devel-x86_64OK312
source / vignettesOK291
linux-release-x86_64OK388
macos-release-arm64OK140
macos-oldrel-arm64OK123
windows-develOK194
windows-releaseOK211
windows-oldrelOK189
wasm-releaseOK216

Exports:check_metadata_namesconvert_LEVEL5_prism_to_gDR_inputconvert_LEVEL6_prism_to_gDR_inputconvert_MAE_to_PSetconvert_pset_to_dfdetect_file_formatget_exception_dataget_test_D300_dataget_test_dataget_test_EnVision_dataget_test_Tecan_dataget_test_tsv_datagetPSetimport_D300is_readable_vload_dataload_manifestload_resultsload_templatesmanifest_pathparse_D300_xmlread_excel_to_dtresult_pathsetEnvForPSetstandardize_record_valuestemplate_path

Dependencies:abindassertthatbackportsbase64encbenchBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbitbit64bitopsbootbroombslibBumpyMatrixcachemcarcarDatacaToolscelestialcellrangercheckmateclicliprclustercodetoolscolorspacecommonmarkcoopCoreGxcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDerivdigestdoBydownloaderdplyrdrcDTevaluatefarverfastmapfastmatchfgseafontawesomeforcatsforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgDRutilsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttpuvigraphIRangesisobandjquerylibjsonlitejsonvalidateKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4lmtestlsamagicaxismagrittrmapprojmapsmarrayMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompMultiAssayExperimentmvtnormNISTunitsnlmenloptrnnetnumDerivopenxlsxotelpbkrtestPharmacoGxpianopillarpkgconfigplotrixplyrpracmaprettyunitsprofmemprogresspromisespurrrqs2quantregR.methodsS3R.ooR.utilsR6RANNrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreadrreadxlreformulasrelationsrematchreshape2riorlangrmarkdownS4ArraysS4VectorsS7sandwichsassscalesSeqinfosetsshinyshinydashboardshinyjsslamsmsnowSnowballCsourcetoolsSparseArraySparseMstatmodstringfishstringistringrSummarizedExperimentsurvivalTH.datatibbletidyrtidyselecttimeDatetinytextzdburcautf8V8vctrsviridisLitevisNetworkvroomwithrwritexlxfunXMLxtableXVectoryamlzipzoo

Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet

Jermiah Joseph, Bartosz Czech

Rendered fromConvertingMAEtoPharmacoSet.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-19
Started: 2023-10-02

Converting PharmacoSet Drug Response Data into gDR object

Jermiah Joseph, Bartosz Czech

Rendered fromConvertingPharmacoSetToGDR.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-19
Started: 2023-06-02

gDRimport

gDR team

Rendered fromgDRimport.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-02-17
Started: 2023-03-29

Readme and manuals

Help Manual

Help pageTopics
Evaluate if template file with single sheet is present, if the name of the sheet is correct and if it can be fixed.check_against_single_template_sheet
are template sheet valid?are_template_sheets_valid
Check metadata against spacescheck_metadata_against_spaces
Check metadata field namescheck_metadata_field_names
Check whether metadata headers are correct and make fixes if neededcheck_metadata_headers
check_metadata_namescheck_metadata_names
Check metadata for required column namescheck_metadata_req_col_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
Correct names of the template sheets (if required)correct_template_sheets
Detect format of results datadetect_file_format
Enhance raw edited EnVision data.tableenhance_raw_edited_EnVision_df
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 properties of EnVision dataget_EnVision_properties
get Excel sheets names for a charvec of files for non-Excel files return 0get_excel_sheet_names
get exception dataget_exception_data
Get names of the sheets expected in templates xlsxget_expected_template_sheets
Get plate info from template xlsxget_plate_info_from_template_xlsx
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 Excel sheetsget_xl_sheets
Get PharmacoSetgetPSet
Import D300import_D300
is_readable_v Check if all paths in vector are readableis_readable_v
Load dataload_data
Load manifestload_manifest
Load resultsload_results
Load EnVision results from xlsxload_results_EnVision
Load results from EnVision_new (CSV and XLSX)load_results_EnVision_new
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
Method manifest_pathmanifest_path manifest_path,gdr_test_data-method
grep wrapper to support multiple patternsmgrepl
Parse D300parse_D300_xml
Read EnVision delimited text filesread_EnVision_delim
Read in single xlsx data from EnVisionread_EnVision_xlsx
Read excel file and transorm it into data.table objectread_excel_to_dt
Read EnVision fileread_in_EnVision_file
read manifest filesread_in_manifest_file
Read in results filesread_in_result_files
read in Tecan dataread_in_results_Tecan
Read in data from xlsx template sheetread_in_template_sheet_xlsx
Read in xlsx template filesread_in_template_xlsx
read in tsv template filesread_in_tsv_template_files
read_ref_dataread_ref_data
Method result_pathresult_path result_path,gdr_test_data-method
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
Method template_pathtemplate_path template_path,gdr_test_data-method
Validate template xlsx datavalidate_template_xlsx