The PharmacoGx package is a popular tool from the Bioconductor project within the field of bioinformatics and computational biology. Whereas the gDR package is a valuable tool that provides the framework for the import, processing, analysism and visualization of high-dimensional drug response data, the PharmacoGx package provides functionality to containerize processed drug response and genomic data to perform pharmacogenomic analyses. The data structure used by PharmacoGx is described as a PharamcoSet class, inherited from CoreGx::CoreSet. Inspired by the SummarizedExperiment class, a new data structure class called the TreatmentResponseExperiment was developed to store drug response data within the PharmacoSet.
In collaboration with the BHKLab, we have developed functionality to convert between the gDR-generated MultiAssayExperiment (MAE) object and the PharmacoSet object (see the ConvertingPharmacoSetToGDR vignette to convert from a PharmacoSet to gDR object).
This workflow assumes that you have already generated a MAE object using the gDR package. We will load in a MAE object generated using the data from the KW. Song et al, 2022 study. This MAE contains two drugs (treatments) and 7 cell lines (samples).
(mae <- qs::qread(
system.file("extdata", "kyung2022mae", "MAE_E2.qs", package = "gDRimport")
)
)
#> A MultiAssayExperiment object of 2 listed
#> experiments with user-defined names and respective classes.
#> Containing an ExperimentList class object of length 2:
#> [1] matrix: SummarizedExperiment with 1 rows and 7 columns
#> [2] single-agent: SummarizedExperiment with 2 rows and 7 columns
#> Functionality:
#> experiments() - obtain the ExperimentList instance
#> colData() - the primary/phenotype DataFrame
#> sampleMap() - the sample coordination DataFrame
#> `$`, `[`, `[[` - extract colData columns, subset, or experiment
#> *Format() - convert into a long or wide DataFrame
#> assays() - convert ExperimentList to a SimpleList of matrices
#> exportClass() - save data to flat filesFirst we will view the experiments and assays within the MultiAssayExperiment object.
gDRutils::MAEpply(mae, assays)
#> $matrix
#> List of length 14
#> names(14): RawTreated Controls Normalized ... CIScore_50 CIScore_80 Metrics
#>
#> $`single-agent`
#> List of length 5
#> names(5): RawTreated Controls Normalized Averaged MetricsWe will now convert the MAE object into a PharmacoSet object. We need to provide a name for the data object, in this example we will use the name of the study.
pset <- convert_MAE_to_PSet(mae, pset_name="Kyung2022")
#> 2024-05-01 17:23:23 Building assay index...
#> 2024-05-01 17:23:23 Joining rowData to assayIndex...
#> 2024-05-01 17:23:24 Joining colData to assayIndex...
#> 2024-05-01 17:23:24 Joining assays to assayIndex...
#> 2024-05-01 17:23:26 Setting assayIndex key...
#> 2024-05-01 17:23:26 Building LongTable...We can now view the PharmacoSet object.
pset
#> <PharmacoSet>
#> Name: Kyung2022
#> Date Created: Wed May 1 17:23:26 2024
#> Number of samples: 7
#> Molecular profiles: <MultiAssayExperiment>
#> ExperimentList class object of length 1:
#> [1] emptySE : SummarizedExperiment with 0 rows and 7 columns
#> Treatment response: <TreatmentResponseExperiment>
#> dim: 3 7
#> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
#> HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
#> CIScore_80 Metrics
#> rownames(3): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
#> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
#> colnames(7): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 ... CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131903_BT-483_Breast_BT-483_unknown_130
#> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
#> metadata(0): noneWe can view information about the drugs and cell lines in the PharmacoSet object using the treatment and sample slots:
head(treatmentInfo(pset))
#> treatmentid
#> 1 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
#> 2 G02001876_Palbociclib_CDK4|CDK6_168
#> 3 G02967907_GDC-0077_PI3K-A_168
#> Gnumber DrugName drug_moa Gnumber_2 DrugName_2 drug_moa_2 DrugName_3
#> 1 G02967907 GDC-0077 PI3K-A G02001876 Palbociclib CDK4|CDK6 vehicle
#> 2 G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 3 G02967907 GDC-0077 PI3K-A <NA> <NA> <NA> <NA>
#> drug_moa_3 Duration
#> 1 vehicle 168
#> 2 <NA> 168
#> 3 <NA> 168
head(sampleInfo(pset))
#> sampleid
#> CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757_MCF-7_Breast_MCF-7_unknown_30
#> CL130218_BT-474_Breast_BT-474_unknown_70 CL130218_BT-474_Breast_BT-474_unknown_70
#> CL130742_T-47D_Breast_T-47D_unknown_60 CL130742_T-47D_Breast_T-47D_unknown_60
#> CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438_CAMA-1_Breast_CAMA-1_unknown_53
#> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873_HCC1428_Breast_HCC1428_unknown_74
#> CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891_EFM-19_Breast_EFM-19_unknown_64
#> clid CellLineName Tissue
#> CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757 MCF-7 Breast
#> CL130218_BT-474_Breast_BT-474_unknown_70 CL130218 BT-474 Breast
#> CL130742_T-47D_Breast_T-47D_unknown_60 CL130742 T-47D Breast
#> CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438 CAMA-1 Breast
#> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873 HCC1428 Breast
#> CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891 EFM-19 Breast
#> parental_identifier subtype
#> CL129757_MCF-7_Breast_MCF-7_unknown_30 MCF-7 unknown
#> CL130218_BT-474_Breast_BT-474_unknown_70 BT-474 unknown
#> CL130742_T-47D_Breast_T-47D_unknown_60 T-47D unknown
#> CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CAMA-1 unknown
#> CL131873_HCC1428_Breast_HCC1428_unknown_74 HCC1428 unknown
#> CL131891_EFM-19_Breast_EFM-19_unknown_64 EFM-19 unknown
#> ReferenceDivisionTime batchid
#> CL129757_MCF-7_Breast_MCF-7_unknown_30 30 1
#> CL130218_BT-474_Breast_BT-474_unknown_70 70 1
#> CL130742_T-47D_Breast_T-47D_unknown_60 60 1
#> CL131438_CAMA-1_Breast_CAMA-1_unknown_53 53 1
#> CL131873_HCC1428_Breast_HCC1428_unknown_74 74 1
#> CL131891_EFM-19_Breast_EFM-19_unknown_64 64 1The TreatmentResponseExperiment is a new class that was developed to store drug response data within the PharmacoSet object. This vignette will cover some basics about this class, however for more information, please refer to the PharmacoSet vignette TreatmentResponseExperiment****.
tre <- treatmentResponse(pset)
head(rownames(tre))
#> [1] "G02001876_Palbociclib_CDK4|CDK6_168"
#> [2] "G02967907_GDC-0077_PI3K-A_168"
#> [3] "G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168"
head(rowData(tre))
#> treatmentid
#> <char>
#> 1: G02001876_Palbociclib_CDK4|CDK6_168
#> 2: G02967907_GDC-0077_PI3K-A_168
#> 3: G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
#> Gnumber DrugName drug_moa Gnumber_2 DrugName_2 drug_moa_2 DrugName_3
#> <char> <char> <char> <char> <char> <char> <char>
#> 1: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 2: G02967907 GDC-0077 PI3K-A <NA> <NA> <NA> <NA>
#> 3: G02967907 GDC-0077 PI3K-A G02001876 Palbociclib CDK4|CDK6 vehicle
#> drug_moa_3 Duration
#> <char> <num>
#> 1: <NA> 168
#> 2: <NA> 168
#> 3: vehicle 168head(colnames(tre))
#> [1] "CL129757_MCF-7_Breast_MCF-7_unknown_30"
#> [2] "CL130218_BT-474_Breast_BT-474_unknown_70"
#> [3] "CL130742_T-47D_Breast_T-47D_unknown_60"
#> [4] "CL131438_CAMA-1_Breast_CAMA-1_unknown_53"
#> [5] "CL131873_HCC1428_Breast_HCC1428_unknown_74"
#> [6] "CL131891_EFM-19_Breast_EFM-19_unknown_64"
head(colData(tre))
#> sampleid clid CellLineName Tissue
#> <char> <char> <char> <char>
#> 1: CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757 MCF-7 Breast
#> 2: CL130218_BT-474_Breast_BT-474_unknown_70 CL130218 BT-474 Breast
#> 3: CL130742_T-47D_Breast_T-47D_unknown_60 CL130742 T-47D Breast
#> 4: CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438 CAMA-1 Breast
#> 5: CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873 HCC1428 Breast
#> 6: CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891 EFM-19 Breast
#> parental_identifier subtype ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: BT-474 unknown 70
#> 3: T-47D unknown 60
#> 4: CAMA-1 unknown 53
#> 5: HCC1428 unknown 74
#> 6: EFM-19 unknown 64data.table SubsettingIn addition to regex queries, a TreatmentResponseExperiment object supports arbitrarily complex subset queries using the data.table API. To access this API, you will need to use the . function, which allows you to pass raw R expressions to be evaluated inside the i and j arguments for dataTable[i, j].
For example if we want to subset to rows where the cell line is “CL131891_EFM-19_Breast_EFM-19_unknown_64” and drug is “G02967907_GDC-0077_PI3K-A_168”.
tre[
.(treatmentid=="G02967907_GDC-0077_PI3K-A_168"), # query on row
.(sampleid=="CL131891_EFM-19_Breast_EFM-19_unknown_64") # query on column
]
#> <TreatmentResponseExperiment>
#> dim: 1 1
#> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
#> HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
#> CIScore_80 Metrics
#> rownames(1): G02967907_GDC-0077_PI3K-A_168
#> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
#> colnames(1): CL131891_EFM-19_Breast_EFM-19_unknown_64
#> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
#> metadata(0): noneWe can also invert matches or subset on other columns in rowData or colData:
tre[
.(treatmentid!="G02967907_GDC-0077_PI3K-A_168"), # query on row
.(sampleid!="CL131891_EFM-19_Breast_EFM-19_unknown_64") # query on column
]
#> <TreatmentResponseExperiment>
#> dim: 2 6
#> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess
#> HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50
#> CIScore_80 Metrics
#> rownames(2): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168
#> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration
#> colnames(6): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131903_BT-483_Breast_BT-483_unknown_130
#> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime
#> metadata(0): noneThe assays can be viewed through the assays function. Each assay has a column “data_type” which references which SummarizedExperiment from the MAE the data corresponds with.
lapply(assays(tre), head)
#> $RawTreated
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type Concentration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 2: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 3: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 4: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 5: <NA> <NA> <NA> <NA> single-agent 0.004572471
#> 6: <NA> <NA> <NA> <NA> single-agent 0.004572471
#> Concentration_2 Barcode ReadoutValue BackgroundValue
#> <num> <char> <num> <num>
#> 1: NA 30190103p 921614 483
#> 2: NA 30190103p 999312 483
#> 3: NA 30190103p 1104556 483
#> 4: NA 30190103p 1122112 483
#> 5: NA 30190103p 874807 483
#> 6: NA 30190103p 994797 483
#> Template WellRow WellColumn record_id masked
#> <char> <char> <char> <int> <lgcl>
#> 1: Template_0077_Palbo_7daytreated.xlsx D 20 2832 FALSE
#> 2: Template_0077_Palbo_7daytreated.xlsx C 20 2831 FALSE
#> 3: Template_0077_Palbo_7daytreated.xlsx D 19 2830 FALSE
#> 4: Template_0077_Palbo_7daytreated.xlsx C 19 2829 FALSE
#> 5: Template_0077_Palbo_7daytreated.xlsx C 18 2835 FALSE
#> 6: Template_0077_Palbo_7daytreated.xlsx D 18 2836 FALSE
#> CorrectedReadout swap_sa i.Gnumber i.DrugName i.drug_moa i.Gnumber_2
#> <num> <lgcl> <char> <char> <char> <char>
#> 1: 921131 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 2: 998829 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 3: 1104073 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 4: 1121629 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 5: 874324 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 6: 994314 NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration i.clid
#> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> 168 CL129757
#> 2: <NA> <NA> <NA> <NA> 168 CL129757
#> 3: <NA> <NA> <NA> <NA> 168 CL129757
#> 4: <NA> <NA> <NA> <NA> 168 CL129757
#> 5: <NA> <NA> <NA> <NA> 168 CL129757
#> 6: <NA> <NA> <NA> <NA> 168 CL129757
#> i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char>
#> 1: MCF-7 Breast MCF-7 unknown
#> 2: MCF-7 Breast MCF-7 unknown
#> 3: MCF-7 Breast MCF-7 unknown
#> 4: MCF-7 Breast MCF-7 unknown
#> 5: MCF-7 Breast MCF-7 unknown
#> 6: MCF-7 Breast MCF-7 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 30
#> 3: 30
#> 4: 30
#> 5: 30
#> 6: 30
#>
#> $Controls
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type control_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> 2: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> 3: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> 4: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> 5: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> 6: <NA> <NA> <NA> <NA> single-agent Day0Readout
#> CorrectedReadout record_id Barcode isDay0 i.Gnumber i.DrugName i.drug_moa
#> <num> <int> <char> <lgcl> <char> <char> <char>
#> 1: 97219 2401 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> 2: 97219 2402 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> 3: 97219 2403 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> 4: 97219 2404 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> 5: 97219 2405 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> 6: 97219 2406 20190103p TRUE G02001876 Palbociclib CDK4|CDK6
#> i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> 168
#> 2: <NA> <NA> <NA> <NA> <NA> 168
#> 3: <NA> <NA> <NA> <NA> <NA> 168
#> 4: <NA> <NA> <NA> <NA> <NA> 168
#> 5: <NA> <NA> <NA> <NA> <NA> 168
#> 6: <NA> <NA> <NA> <NA> <NA> 168
#> i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char> <char>
#> 1: CL129757 MCF-7 Breast MCF-7 unknown
#> 2: CL129757 MCF-7 Breast MCF-7 unknown
#> 3: CL129757 MCF-7 Breast MCF-7 unknown
#> 4: CL129757 MCF-7 Breast MCF-7 unknown
#> 5: CL129757 MCF-7 Breast MCF-7 unknown
#> 6: CL129757 MCF-7 Breast MCF-7 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 30
#> 3: 30
#> 4: 30
#> 5: 30
#> 6: 30
#>
#> $Normalized
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type Concentration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 2: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 3: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 4: <NA> <NA> <NA> <NA> single-agent 0.001524158
#> 5: <NA> <NA> <NA> <NA> single-agent 0.004572471
#> 6: <NA> <NA> <NA> <NA> single-agent 0.004572471
#> Concentration_2 masked normalization_type x i.Gnumber i.DrugName
#> <num> <lgcl> <fctr> <num> <char> <char>
#> 1: NA FALSE RV 0.8253 G02001876 Palbociclib
#> 2: NA FALSE RV 0.8949 G02001876 Palbociclib
#> 3: NA FALSE RV 0.9892 G02001876 Palbociclib
#> 4: NA FALSE RV 1.0049 G02001876 Palbociclib
#> 5: NA FALSE RV 0.7833 G02001876 Palbociclib
#> 6: NA FALSE RV 0.8908 G02001876 Palbociclib
#> i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
#> <char> <char> <char> <char> <char> <char>
#> 1: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 2: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 3: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 4: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 5: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 6: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> i.Duration i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <num> <char> <char> <char> <char> <char>
#> 1: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 2: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 3: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 4: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 5: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 6: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 30
#> 3: 30
#> 4: 30
#> 5: 30
#> 6: 30
#>
#> $Averaged
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <fctr>
#> 1: <NA> <NA> <NA> <NA> single-agent RV
#> 2: <NA> <NA> <NA> <NA> single-agent GR
#> 3: <NA> <NA> <NA> <NA> single-agent RV
#> 4: <NA> <NA> <NA> <NA> single-agent GR
#> 5: <NA> <NA> <NA> <NA> single-agent RV
#> 6: <NA> <NA> <NA> <NA> single-agent GR
#> Concentration Concentration_2 x x_std i.Gnumber i.DrugName
#> <num> <num> <num> <num> <char> <char>
#> 1: 0.001524158 NA 0.928575 0.08426274 G02001876 Palbociclib
#> 2: 0.001524158 NA 0.952225 0.05675581 G02001876 Palbociclib
#> 3: 0.004572471 NA 0.885050 0.07091133 G02001876 Palbociclib
#> 4: 0.004572471 NA 0.923000 0.04998000 G02001876 Palbociclib
#> 5: 0.013717406 NA 0.843800 0.05585201 G02001876 Palbociclib
#> 6: 0.013717406 NA 0.894475 0.04037973 G02001876 Palbociclib
#> i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
#> <char> <char> <char> <char> <char> <char>
#> 1: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 2: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 3: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 4: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 5: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 6: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> i.Duration i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <num> <char> <char> <char> <char> <char>
#> 1: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 2: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 3: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 4: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 5: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 6: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 30
#> 3: 30
#> 4: 30
#> 5: 30
#> 6: 30
#>
#> $SmoothMatrix
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type Concentration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent NA
#> 2: <NA> <NA> <NA> <NA> single-agent NA
#> 3: <NA> <NA> <NA> <NA> single-agent NA
#> 4: <NA> <NA> <NA> <NA> single-agent NA
#> 5: <NA> <NA> <NA> <NA> single-agent NA
#> 6: <NA> <NA> <NA> <NA> single-agent NA
#> Concentration_2 x normalization_type i.Gnumber i.DrugName i.drug_moa
#> <num> <num> <char> <char> <char> <char>
#> 1: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 2: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 3: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 4: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 5: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> 6: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> 168
#> 2: <NA> <NA> <NA> <NA> <NA> 168
#> 3: <NA> <NA> <NA> <NA> <NA> 168
#> 4: <NA> <NA> <NA> <NA> <NA> 168
#> 5: <NA> <NA> <NA> <NA> <NA> 168
#> 6: <NA> <NA> <NA> <NA> <NA> 168
#> i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char> <char>
#> 1: CL129757 MCF-7 Breast MCF-7 unknown
#> 2: CL130742 T-47D Breast T-47D unknown
#> 3: CL131873 HCC1428 Breast HCC1428 unknown
#> 4: CL131903 BT-483 Breast BT-483 unknown
#> 5: CL130218 BT-474 Breast BT-474 unknown
#> 6: CL131438 CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $BlissExcess
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type Concentration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent NA
#> 2: <NA> <NA> <NA> <NA> single-agent NA
#> 3: <NA> <NA> <NA> <NA> single-agent NA
#> 4: <NA> <NA> <NA> <NA> single-agent NA
#> 5: <NA> <NA> <NA> <NA> single-agent NA
#> 6: <NA> <NA> <NA> <NA> single-agent NA
#> Concentration_2 x normalization_type i.Gnumber i.DrugName i.drug_moa
#> <num> <num> <char> <char> <char> <char>
#> 1: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 2: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 3: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 4: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 5: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> 6: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> 168
#> 2: <NA> <NA> <NA> <NA> <NA> 168
#> 3: <NA> <NA> <NA> <NA> <NA> 168
#> 4: <NA> <NA> <NA> <NA> <NA> 168
#> 5: <NA> <NA> <NA> <NA> <NA> 168
#> 6: <NA> <NA> <NA> <NA> <NA> 168
#> i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char> <char>
#> 1: CL129757 MCF-7 Breast MCF-7 unknown
#> 2: CL130742 T-47D Breast T-47D unknown
#> 3: CL131873 HCC1428 Breast HCC1428 unknown
#> 4: CL131903 BT-483 Breast BT-483 unknown
#> 5: CL130218 BT-474 Breast BT-474 unknown
#> 6: CL131438 CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $HSAExcess
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type Concentration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent NA
#> 2: <NA> <NA> <NA> <NA> single-agent NA
#> 3: <NA> <NA> <NA> <NA> single-agent NA
#> 4: <NA> <NA> <NA> <NA> single-agent NA
#> 5: <NA> <NA> <NA> <NA> single-agent NA
#> 6: <NA> <NA> <NA> <NA> single-agent NA
#> Concentration_2 x normalization_type i.Gnumber i.DrugName i.drug_moa
#> <num> <num> <char> <char> <char> <char>
#> 1: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 2: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 3: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 4: NA NA <NA> G02001876 Palbociclib CDK4|CDK6
#> 5: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> 6: NA NA <NA> G02967907 GDC-0077 PI3K-A
#> i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> 168
#> 2: <NA> <NA> <NA> <NA> <NA> 168
#> 3: <NA> <NA> <NA> <NA> <NA> 168
#> 4: <NA> <NA> <NA> <NA> <NA> 168
#> 5: <NA> <NA> <NA> <NA> <NA> 168
#> 6: <NA> <NA> <NA> <NA> <NA> 168
#> i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char> <char>
#> 1: CL129757 MCF-7 Breast MCF-7 unknown
#> 2: CL130742 T-47D Breast T-47D unknown
#> 3: CL131873 HCC1428 Breast HCC1428 unknown
#> 4: CL131903 BT-483 Breast BT-483 unknown
#> 5: CL130218 BT-474 Breast BT-474 unknown
#> 6: CL131438 CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $all_iso_points
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
#> <char> <char> <char> <char> <char> <char>
#> 1: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 2: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 3: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 4: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 5: G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> 6: G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <char> <num> <char> <char> <char>
#> 1: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> <NA> 168 CL130742 T-47D Breast
#> 3: <NA> <NA> 168 CL131873 HCC1428 Breast
#> 4: <NA> <NA> 168 CL131903 BT-483 Breast
#> 5: <NA> <NA> 168 CL130218 BT-474 Breast
#> 6: <NA> <NA> 168 CL131438 CAMA-1 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime x
#> <char> <char> <num> <lgcl>
#> 1: MCF-7 unknown 30 NA
#> 2: T-47D unknown 60 NA
#> 3: HCC1428 unknown 74 NA
#> 4: BT-483 unknown 130 NA
#> 5: BT-474 unknown 70 NA
#> 6: CAMA-1 unknown 53 NA
#>
#> $isobolograms
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
#> <char> <char> <char> <char> <char> <char>
#> 1: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 2: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 3: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 4: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 5: G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> 6: G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <char> <num> <char> <char> <char>
#> 1: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> <NA> 168 CL130742 T-47D Breast
#> 3: <NA> <NA> 168 CL131873 HCC1428 Breast
#> 4: <NA> <NA> 168 CL131903 BT-483 Breast
#> 5: <NA> <NA> 168 CL130218 BT-474 Breast
#> 6: <NA> <NA> 168 CL131438 CAMA-1 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime x
#> <char> <char> <num> <lgcl>
#> 1: MCF-7 unknown 30 NA
#> 2: T-47D unknown 60 NA
#> 3: HCC1428 unknown 74 NA
#> 4: BT-483 unknown 130 NA
#> 5: BT-474 unknown 70 NA
#> 6: CAMA-1 unknown 53 NA
#>
#> $BlissScore
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
#> <num> <char> <char> <char> <char> <char> <char>
#> 1: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 2: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 3: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 4: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 5: NA G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> 6: NA G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <char> <num> <char> <char> <char>
#> 1: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> <NA> 168 CL130742 T-47D Breast
#> 3: <NA> <NA> 168 CL131873 HCC1428 Breast
#> 4: <NA> <NA> 168 CL131903 BT-483 Breast
#> 5: <NA> <NA> 168 CL130218 BT-474 Breast
#> 6: <NA> <NA> 168 CL131438 CAMA-1 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: T-47D unknown 60
#> 3: HCC1428 unknown 74
#> 4: BT-483 unknown 130
#> 5: BT-474 unknown 70
#> 6: CAMA-1 unknown 53
#>
#> $HSAScore
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2
#> <num> <char> <char> <char> <char> <char> <char>
#> 1: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 2: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 3: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 4: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 5: NA G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> 6: NA G02967907 GDC-0077 PI3K-A <NA> <NA> <NA>
#> i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <char> <num> <char> <char> <char>
#> 1: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> <NA> 168 CL130742 T-47D Breast
#> 3: <NA> <NA> 168 CL131873 HCC1428 Breast
#> 4: <NA> <NA> 168 CL131903 BT-483 Breast
#> 5: <NA> <NA> 168 CL130218 BT-474 Breast
#> 6: <NA> <NA> 168 CL131438 CAMA-1 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: T-47D unknown 60
#> 3: HCC1428 unknown 74
#> 4: BT-483 unknown 130
#> 5: BT-474 unknown 70
#> 6: CAMA-1 unknown 53
#>
#> $CIScore_50
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
#> <lgcl> <char> <char> <char> <char> <char>
#> 1: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 2: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 3: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 4: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 5: NA G02967907 GDC-0077 PI3K-A <NA> <NA>
#> 6: NA G02967907 GDC-0077 PI3K-A <NA> <NA>
#> i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName
#> <char> <char> <char> <num> <char> <char>
#> 1: <NA> <NA> <NA> 168 CL129757 MCF-7
#> 2: <NA> <NA> <NA> 168 CL130742 T-47D
#> 3: <NA> <NA> <NA> 168 CL131873 HCC1428
#> 4: <NA> <NA> <NA> 168 CL131903 BT-483
#> 5: <NA> <NA> <NA> 168 CL130218 BT-474
#> 6: <NA> <NA> <NA> 168 CL131438 CAMA-1
#> i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <char> <num>
#> 1: Breast MCF-7 unknown 30
#> 2: Breast T-47D unknown 60
#> 3: Breast HCC1428 unknown 74
#> 4: Breast BT-483 unknown 130
#> 5: Breast BT-474 unknown 70
#> 6: Breast CAMA-1 unknown 53
#>
#> $CIScore_80
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type normalization_type
#> <char> <char> <char> <char> <char> <char>
#> 1: <NA> <NA> <NA> <NA> single-agent <NA>
#> 2: <NA> <NA> <NA> <NA> single-agent <NA>
#> 3: <NA> <NA> <NA> <NA> single-agent <NA>
#> 4: <NA> <NA> <NA> <NA> single-agent <NA>
#> 5: <NA> <NA> <NA> <NA> single-agent <NA>
#> 6: <NA> <NA> <NA> <NA> single-agent <NA>
#> x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
#> <lgcl> <char> <char> <char> <char> <char>
#> 1: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 2: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 3: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 4: NA G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 5: NA G02967907 GDC-0077 PI3K-A <NA> <NA>
#> 6: NA G02967907 GDC-0077 PI3K-A <NA> <NA>
#> i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration i.clid i.CellLineName
#> <char> <char> <char> <num> <char> <char>
#> 1: <NA> <NA> <NA> 168 CL129757 MCF-7
#> 2: <NA> <NA> <NA> 168 CL130742 T-47D
#> 3: <NA> <NA> <NA> 168 CL131873 HCC1428
#> 4: <NA> <NA> <NA> 168 CL131903 BT-483
#> 5: <NA> <NA> <NA> 168 CL130218 BT-474
#> 6: <NA> <NA> <NA> 168 CL131438 CAMA-1
#> i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <char> <num>
#> 1: Breast MCF-7 unknown 30
#> 2: Breast T-47D unknown 60
#> 3: Breast HCC1428 unknown 74
#> 4: Breast BT-483 unknown 130
#> 5: Breast BT-474 unknown 70
#> 6: Breast CAMA-1 unknown 53
#>
#> $Metrics
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid DrugName DrugName_2 DrugName_3 Duration Gnumber
#> <char> <char> <char> <char> <char> <num> <char>
#> 1: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> 6: <NA> <NA> <NA> <NA> <NA> NA <NA>
#> Gnumber_2 drug_moa drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime
#> <char> <char> <char> <char> <char> <num>
#> 1: <NA> <NA> <NA> <NA> <NA> NA
#> 2: <NA> <NA> <NA> <NA> <NA> NA
#> 3: <NA> <NA> <NA> <NA> <NA> NA
#> 4: <NA> <NA> <NA> <NA> <NA> NA
#> 5: <NA> <NA> <NA> <NA> <NA> NA
#> 6: <NA> <NA> <NA> <NA> <NA> NA
#> Tissue clid parental_identifier subtype data_type x_mean x_AOC
#> <char> <char> <char> <char> <char> <num> <num>
#> 1: <NA> <NA> <NA> <NA> single-agent 0.4766169 0.5233831
#> 2: <NA> <NA> <NA> <NA> single-agent 0.6438030 0.3561970
#> 3: <NA> <NA> <NA> <NA> single-agent 0.5797408 0.4202592
#> 4: <NA> <NA> <NA> <NA> single-agent 0.4888085 0.5111915
#> 5: <NA> <NA> <NA> <NA> single-agent 0.6458536 0.3541464
#> 6: <NA> <NA> <NA> <NA> single-agent 0.4821213 0.5178787
#> x_AOC_range xc50 x_max ec50 x_inf x_0 h
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.5685724 0.07649828 0.107050 0.06354470 0.08684205 1 1.0283168
#> 2: 0.3828886 0.26119890 0.281750 0.09897928 0.32080324 1 1.0574543
#> 3: 0.4560827 0.10802210 0.207125 0.08784832 0.21933259 1 2.7932767
#> 4: 0.5620006 0.06629065 0.111625 0.05911087 0.12311310 1 2.4657832
#> 5: 0.3770687 0.26781723 0.228300 0.13626047 0.27577126 1 1.1867664
#> 6: 0.5639825 0.06294109 0.148225 0.04029515 0.16592442 1 0.9041923
#> r2 x_sd_avg fit_type maxlog10Concentration N_conc
#> <num> <num> <char> <num> <int>
#> 1: 0.9853800 0.05272629 DRC3pHillFitModelFixS0 1 10
#> 2: 0.9465590 0.07259453 DRC3pHillFitModelFixS0 1 10
#> 3: 0.9787945 0.06655135 DRC3pHillFitModelFixS0 1 10
#> 4: 0.9946671 0.07915584 DRC3pHillFitModelFixS0 1 10
#> 5: 0.9616801 0.06463053 DRC3pHillFitModelFixS0 1 10
#> 6: 0.9740112 0.05594059 DRC3pHillFitModelFixS0 1 10
#> normalization_type fit_source cotrt_value source i.Gnumber i.DrugName
#> <char> <char> <num> <char> <char> <char>
#> 1: RV gDR NA <NA> G02001876 Palbociclib
#> 2: RV gDR NA <NA> G02001876 Palbociclib
#> 3: RV gDR NA <NA> G02001876 Palbociclib
#> 4: RV gDR NA <NA> G02001876 Palbociclib
#> 5: RV gDR NA <NA> G02001876 Palbociclib
#> 6: RV gDR NA <NA> G02001876 Palbociclib
#> i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
#> <char> <char> <char> <char> <char> <char>
#> 1: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 2: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 3: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 4: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 5: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 6: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> i.Duration i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <num> <char> <char> <char> <char> <char>
#> 1: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 2: 168 CL130218 BT-474 Breast BT-474 unknown
#> 3: 168 CL130742 T-47D Breast T-47D unknown
#> 4: 168 CL131438 CAMA-1 Breast CAMA-1 unknown
#> 5: 168 CL131873 HCC1428 Breast HCC1428 unknown
#> 6: 168 CL131891 EFM-19 Breast EFM-19 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 70
#> 3: 60
#> 4: 53
#> 5: 74
#> 6: 64assayNames(tre)
#> [1] "RawTreated" "Controls" "Normalized" "Averaged"
#> [5] "SmoothMatrix" "BlissExcess" "HSAExcess" "all_iso_points"
#> [9] "isobolograms" "BlissScore" "HSAScore" "CIScore_50"
#> [13] "CIScore_80" "Metrics"head(assay(tre, "Metrics"),3)
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid
#> <char> <char>
#> 1: G02001876_Palbociclib_CDK4|CDK6_168 CL129757_MCF-7_Breast_MCF-7_unknown_30
#> 2: G02001876_Palbociclib_CDK4|CDK6_168 CL130218_BT-474_Breast_BT-474_unknown_70
#> 3: G02001876_Palbociclib_CDK4|CDK6_168 CL130742_T-47D_Breast_T-47D_unknown_60
#> DrugName DrugName_2 DrugName_3 Duration Gnumber Gnumber_2 drug_moa
#> <char> <char> <char> <num> <char> <char> <char>
#> 1: Palbociclib <NA> <NA> 168 G02001876 <NA> CDK4|CDK6
#> 2: Palbociclib <NA> <NA> 168 G02001876 <NA> CDK4|CDK6
#> 3: Palbociclib <NA> <NA> 168 G02001876 <NA> CDK4|CDK6
#> drug_moa_2 drug_moa_3 CellLineName ReferenceDivisionTime Tissue clid
#> <char> <char> <char> <num> <char> <char>
#> 1: <NA> <NA> MCF-7 30 Breast CL129757
#> 2: <NA> <NA> BT-474 70 Breast CL130218
#> 3: <NA> <NA> T-47D 60 Breast CL130742
#> parental_identifier subtype data_type x_mean x_AOC x_AOC_range
#> <char> <char> <char> <num> <num> <num>
#> 1: MCF-7 unknown single-agent 0.4774514 0.5225486 0.5592516
#> 2: BT-474 unknown single-agent 0.5916887 0.4083113 0.4338082
#> 3: T-47D unknown single-agent 0.5478704 0.4521296 0.4876840
#> xc50 x_max ec50 x_inf x_0 h r2
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.1100133 -0.017025 0.1161741 -0.03117468 1 1.1100114 0.9880388
#> 2: 0.2091202 0.114275 0.1360264 0.16571556 1 0.9361851 0.9555750
#> 3: 0.1164343 0.111425 0.1033672 0.13053185 1 2.5415386 0.9815621
#> x_sd_avg fit_type maxlog10Concentration N_conc
#> <num> <char> <num> <int>
#> 1: 0.05887778 DRC3pHillFitModelFixS0 1 10
#> 2: 0.08197778 DRC3pHillFitModelFixS0 1 10
#> 3: 0.06581980 DRC3pHillFitModelFixS0 1 10
#> normalization_type fit_source cotrt_value source i.Gnumber i.DrugName
#> <char> <char> <num> <char> <char> <char>
#> 1: GR gDR NA <NA> G02001876 Palbociclib
#> 2: GR gDR NA <NA> G02001876 Palbociclib
#> 3: GR gDR NA <NA> G02001876 Palbociclib
#> i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3
#> <char> <char> <char> <char> <char> <char>
#> 1: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 2: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> 3: CDK4|CDK6 <NA> <NA> <NA> <NA> <NA>
#> i.Duration i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <num> <char> <char> <char> <char> <char>
#> 1: 168 CL129757 MCF-7 Breast MCF-7 unknown
#> 2: 168 CL130218 BT-474 Breast BT-474 unknown
#> 3: 168 CL130742 T-47D Breast T-47D unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 70
#> 3: 60sessionInfo()
#> R version 4.4.0 RC (2024-04-16 r86468)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] MultiAssayExperiment_1.31.0 gDRimport_1.3.0
#> [3] PharmacoGx_3.9.0 CoreGx_2.9.0
#> [5] SummarizedExperiment_1.35.0 Biobase_2.65.0
#> [7] GenomicRanges_1.57.0 GenomeInfoDb_1.41.0
#> [9] IRanges_2.39.0 S4Vectors_0.43.0
#> [11] MatrixGenerics_1.17.0 matrixStats_1.3.0
#> [13] BiocGenerics_0.51.0
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 rlang_1.1.3 magrittr_2.0.3
#> [4] shinydashboard_0.7.2 compiler_4.4.0 vctrs_0.6.5
#> [7] reshape2_1.4.4 relations_0.6-13 stringr_1.5.1
#> [10] pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1
#> [13] backports_1.4.1 XVector_0.45.0 caTools_1.18.2
#> [16] utf8_1.2.4 promises_1.3.0 rmarkdown_2.26
#> [19] UCSC.utils_1.1.0 coop_0.6-3 xfun_0.43
#> [22] zlibbioc_1.51.0 cachem_1.0.8 jsonlite_1.8.8
#> [25] SnowballC_0.7.1 later_1.3.2 DelayedArray_0.31.0
#> [28] BiocParallel_1.39.0 parallel_4.4.0 sets_1.0-25
#> [31] cluster_2.1.6 R6_2.5.1 stringi_1.8.3
#> [34] bslib_0.7.0 RColorBrewer_1.1-3 qs_0.26.1
#> [37] limma_3.61.0 boot_1.3-30 jquerylib_0.1.4
#> [40] Rcpp_1.0.12 knitr_1.46 downloader_0.4
#> [43] httpuv_1.6.15 Matrix_1.7-0 igraph_2.0.3
#> [46] tidyselect_1.2.1 abind_1.4-5 yaml_2.3.8
#> [49] stringfish_0.16.0 gplots_3.1.3.1 codetools_0.2-20
#> [52] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9
#> [55] shiny_1.8.1.1 BumpyMatrix_1.13.0 evaluate_0.23
#> [58] RcppParallel_5.1.7 bench_1.1.3 pillar_1.9.0
#> [61] lsa_0.73.3 KernSmooth_2.23-22 checkmate_2.3.1
#> [64] DT_0.33 shinyjs_2.1.0 piano_2.21.0
#> [67] generics_0.1.3 ggplot2_3.5.1 munsell_0.5.1
#> [70] scales_1.3.0 RApiSerialize_0.1.2 gtools_3.9.5
#> [73] xtable_1.8-4 marray_1.83.0 glue_1.7.0
#> [76] slam_0.1-50 tools_4.4.0 data.table_1.15.4
#> [79] gDRutils_1.3.0 fgsea_1.31.0 visNetwork_2.1.2
#> [82] fastmatch_1.1-4 cowplot_1.1.3 grid_4.4.0
#> [85] colorspace_2.1-0 GenomeInfoDbData_1.2.12 cli_3.6.2
#> [88] fansi_1.0.6 S4Arrays_1.5.0 dplyr_1.1.4
#> [91] gtable_0.3.5 sass_0.4.9 digest_0.6.35
#> [94] SparseArray_1.5.0 htmlwidgets_1.6.4 htmltools_0.5.8.1
#> [97] lifecycle_1.0.4 httr_1.4.7 statmod_1.5.0
#> [100] mime_0.12