Package: gDRcore 1.5.4

Arkadiusz Gladki

gDRcore: Processing functions and interface to process and analyze drug dose-response data

This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

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

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gDRcore.pdf |gDRcore.html✨
gDRcore/json (API)
NEWS

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

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

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:gDRcore-1.5.3(bioc 3.21)gDRcore-1.4.0(bioc 3.20)

softwareshinyappscpp

7.02 score 1 stars 1 packages 4 scripts 160 downloads 38 exports 110 dependencies

Last updated 1 months agofrom:f6235edac2. Checks:4 OK, 2 NOTE, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 24 2025
R-4.5-win-x86_64NOTEJan 24 2025
R-4.5-linux-x86_64NOTEJan 24 2025
R-4.4-win-x86_64OKJan 24 2025
R-4.4-mac-x86_64OKJan 24 2025
R-4.4-mac-aarch64OKJan 24 2025
R-4.3-win-x86_64ERRORJan 25 2025
R-4.3-mac-x86_64ERRORJan 25 2025
R-4.3-mac-aarch64ERRORJan 25 2025

Exports:.standardize_concannotate_dt_with_cell_lineannotate_dt_with_drugaverage_SEcalculate_Blisscalculate_endpt_GR_valuecalculate_excesscalculate_GR_valuecalculate_HSAcalculate_scorecalculate_time_dep_GR_valuecleanup_metadataconvert_mae_to_raw_dataconvert_se_to_raw_datacreate_and_normalize_SEcreate_SEdata_modelfit_SEfit_SE.combinationsget_cell_line_annotationget_cellline_annotation_from_dtget_default_nested_identifiersget_drug_annotationget_drug_annotation_from_dtgrr_matchesidentify_data_typeidentify_keysmap_conc_to_standardized_concmap_dfmap_ids_to_fitsmerge_datanormalize_SEprepare_inputprocess_perturbationsreplace_conc_with_standardized_concrunDrugResponseProcessingPipelinesplit_raw_datatest_synthetic_data

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbootbroomBumpyMatrixcarcarDatacheckmateclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArrayDerivdoBydplyrdrcfansifarverformatRFormulafutile.loggerfutile.optionsgDRutilsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablegtoolshttrIRangesisobandjsonlitejsonvalidatelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmultcompMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotrixpurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS4ArraysS4VectorssandwichscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsysTH.datatibbletidyrtidyselectUCSC.utilsutf8V8vctrsviridisLitewithrXVectorzoo

gDR annotation

gDR team

Rendered fromgDR-annotation.Rmdusingknitr::rmarkdownon Jan 24 2025.

Last update: 2024-10-28
Started: 2024-04-23

gDRcore

gDR team

Rendered fromgDRcore.Rmdusingknitr::rmarkdownon Jan 24 2025.

Last update: 2024-03-13
Started: 2023-03-31

gDR -- data model

gDR team

Rendered fromgDR-data-model.Rmdusingknitr::rmarkdownon Jan 24 2025.

Last update: 2024-02-05
Started: 2024-02-05

Readme and manuals

Help Manual

Help pageTopics
Map references.map_references
Standardize concentration values..standardize_conc
annotate_dt_with_cell_lineannotate_dt_with_cell_line
annotate_dt_with_drugannotate_dt_with_drug
Run drug response processing pipelineaverage_SE create_and_normalize_SE create_SE fit_SE normalize_SE runDrugResponseProcessingPipeline runDrugResponseProcessingPipelineFxns
Calculate the difference between values in two data.tablescalculate_excess
Calculate a GR value.calculate_endpt_GR_value calculate_GR_value calculate_time_dep_GR_value
Calculate a metric for combination data..calculate_matrix_metric calculate_Bliss calculate_HSA calculate_matrix_metric
Calculate score for HSA and Blisscalculate_score
cleanup_metadatacleanup_metadata
Transform mae into raw dataconvert_mae_to_raw_data
Transform se into raw_dataconvert_se_to_raw_data
Detect model of datadata_model
Detect model of data from experiment namedata_model.character
Detect model of data in data.tabledata_model.data.table
fit_SE for combination screensfit_SE.combinations
get info about created/present assays in SE at the given pipeline stepget_assays_per_pipeline_step
get_cell_line_annotationget_cell_line_annotation
Retrieve the cell line annotation from the annotated dt inputget_cellline_annotation_from_dt
Get default nested identifiersget_default_nested_identifiers get_default_nested_identifiers.data.table get_default_nested_identifiers.SummarizedExperiment
get_drug_annotationget_drug_annotation
Retrieve the drug annotation from the annotated dt inputget_drug_annotation_from_dt
Value Matchinggrr_matches
Identify type of dataidentify_data_type
identify_keysidentify_keys
Create a mapping of concentrations to standardized concentrations.map_conc_to_standardized_conc
Map treated conditions to their respective references.map_df
Get predicted values for a given fit and input.map_ids_to_fits
Identify untreated rows based on Drug treatment alonemap_untreated
merge_datamerge_data
Order_result_dforder_result_df
Prepare input data common for all experimentsprepare_input
Prepare input data common for all experimentsprepare_input.data.table
Prepare input data common for all experimentsprepare_input.MultiAssayExperiment
Cleanup additional perturbations in the data.tableprocess_perturbations
Standardize concentrations.replace_conc_with_standardized_conc
Split raw data into list based on the data typessplit_raw_data
Testing synthetic data form gDRtestData packagetest_synthetic_data