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")
#> 2024-04-30 23:51:17 Building assay index...
#> 2024-04-30 23:51:17 Joining rowData to assayIndex...
#> 2024-04-30 23:51:17 Joining colData to assayIndex...
#> 2024-04-30 23:51:18 Joining assays to assayIndex...
#> 2024-04-30 23:51:19 Setting assayIndex key...
#> 2024-04-30 23:51:20 Building LongTable...We can now view the PharmacoSet object.
pset
#> <PharmacoSet>
#> Name: Kyung2022
#> Date Created: Tue Apr 30 23:51:20 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 drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> Concentration Concentration_2 Barcode ReadoutValue BackgroundValue
#> <num> <num> <char> <num> <num>
#> 1: 0.001524158 NA 30190103p 921614 483
#> 2: 0.001524158 NA 30190103p 999312 483
#> 3: 0.001524158 NA 30190103p 1104556 483
#> 4: 0.001524158 NA 30190103p 1122112 483
#> 5: 0.004572471 NA 30190103p 874807 483
#> 6: 0.004572471 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 drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> control_type CorrectedReadout record_id Barcode isDay0 i.Gnumber
#> <char> <num> <int> <char> <lgcl> <char>
#> 1: Day0Readout 97219 2401 20190103p TRUE G02001876
#> 2: Day0Readout 97219 2402 20190103p TRUE G02001876
#> 3: Day0Readout 97219 2403 20190103p TRUE G02001876
#> 4: Day0Readout 97219 2404 20190103p TRUE G02001876
#> 5: Day0Readout 97219 2405 20190103p TRUE G02001876
#> 6: Day0Readout 97219 2406 20190103p TRUE G02001876
#> i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3
#> <char> <char> <char> <char> <char> <char>
#> 1: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 2: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 3: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 4: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 5: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 6: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <num> <char> <char> <char>
#> 1: <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> 168 CL129757 MCF-7 Breast
#> 3: <NA> 168 CL129757 MCF-7 Breast
#> 4: <NA> 168 CL129757 MCF-7 Breast
#> 5: <NA> 168 CL129757 MCF-7 Breast
#> 6: <NA> 168 CL129757 MCF-7 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: MCF-7 unknown 30
#> 3: MCF-7 unknown 30
#> 4: MCF-7 unknown 30
#> 5: MCF-7 unknown 30
#> 6: MCF-7 unknown 30
#>
#> $Normalized
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> Concentration Concentration_2 masked normalization_type x i.Gnumber
#> <num> <num> <lgcl> <fctr> <num> <char>
#> 1: 0.001524158 NA FALSE RV 0.8253 G02001876
#> 2: 0.001524158 NA FALSE RV 0.8949 G02001876
#> 3: 0.001524158 NA FALSE RV 0.9892 G02001876
#> 4: 0.001524158 NA FALSE RV 1.0049 G02001876
#> 5: 0.004572471 NA FALSE RV 0.7833 G02001876
#> 6: 0.004572471 NA FALSE RV 0.8908 G02001876
#> i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3
#> <char> <char> <char> <char> <char> <char>
#> 1: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 2: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 3: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 4: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 5: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> 6: Palbociclib CDK4|CDK6 <NA> <NA> <NA> <NA>
#> i.drug_moa_3 i.Duration i.clid i.CellLineName i.Tissue
#> <char> <num> <char> <char> <char>
#> 1: <NA> 168 CL129757 MCF-7 Breast
#> 2: <NA> 168 CL129757 MCF-7 Breast
#> 3: <NA> 168 CL129757 MCF-7 Breast
#> 4: <NA> 168 CL129757 MCF-7 Breast
#> 5: <NA> 168 CL129757 MCF-7 Breast
#> 6: <NA> 168 CL129757 MCF-7 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: MCF-7 unknown 30
#> 3: MCF-7 unknown 30
#> 4: MCF-7 unknown 30
#> 5: MCF-7 unknown 30
#> 6: MCF-7 unknown 30
#>
#> $Averaged
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type Concentration Concentration_2 x x_std
#> <fctr> <num> <num> <num> <num>
#> 1: RV 0.001524158 NA 0.928575 0.08426274
#> 2: GR 0.001524158 NA 0.952225 0.05675581
#> 3: RV 0.004572471 NA 0.885050 0.07091133
#> 4: GR 0.004572471 NA 0.923000 0.04998000
#> 5: RV 0.013717406 NA 0.843800 0.05585201
#> 6: GR 0.013717406 NA 0.894475 0.04037973
#> 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: G02001876 Palbociclib CDK4|CDK6 <NA> <NA> <NA>
#> 6: G02001876 Palbociclib CDK4|CDK6 <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 CL129757 MCF-7 Breast
#> 3: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 4: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 5: <NA> <NA> 168 CL129757 MCF-7 Breast
#> 6: <NA> <NA> 168 CL129757 MCF-7 Breast
#> i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <num>
#> 1: MCF-7 unknown 30
#> 2: MCF-7 unknown 30
#> 3: MCF-7 unknown 30
#> 4: MCF-7 unknown 30
#> 5: MCF-7 unknown 30
#> 6: MCF-7 unknown 30
#>
#> $SmoothMatrix
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> Concentration Concentration_2 x normalization_type i.Gnumber i.DrugName
#> <num> <num> <num> <char> <char> <char>
#> 1: NA NA NA <NA> G02001876 Palbociclib
#> 2: NA NA NA <NA> G02001876 Palbociclib
#> 3: NA NA NA <NA> G02001876 Palbociclib
#> 4: NA NA NA <NA> G02001876 Palbociclib
#> 5: NA NA NA <NA> G02967907 GDC-0077
#> 6: NA NA NA <NA> G02967907 GDC-0077
#> 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: PI3K-A <NA> <NA> <NA> <NA> <NA>
#> 6: PI3K-A <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 CL130742 T-47D Breast T-47D unknown
#> 3: 168 CL131873 HCC1428 Breast HCC1428 unknown
#> 4: 168 CL131903 BT-483 Breast BT-483 unknown
#> 5: 168 CL130218 BT-474 Breast BT-474 unknown
#> 6: 168 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 drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> Concentration Concentration_2 x normalization_type i.Gnumber i.DrugName
#> <num> <num> <num> <char> <char> <char>
#> 1: NA NA NA <NA> G02001876 Palbociclib
#> 2: NA NA NA <NA> G02001876 Palbociclib
#> 3: NA NA NA <NA> G02001876 Palbociclib
#> 4: NA NA NA <NA> G02001876 Palbociclib
#> 5: NA NA NA <NA> G02967907 GDC-0077
#> 6: NA NA NA <NA> G02967907 GDC-0077
#> 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: PI3K-A <NA> <NA> <NA> <NA> <NA>
#> 6: PI3K-A <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 CL130742 T-47D Breast T-47D unknown
#> 3: 168 CL131873 HCC1428 Breast HCC1428 unknown
#> 4: 168 CL131903 BT-483 Breast BT-483 unknown
#> 5: 168 CL130218 BT-474 Breast BT-474 unknown
#> 6: 168 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 drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> Concentration Concentration_2 x normalization_type i.Gnumber i.DrugName
#> <num> <num> <num> <char> <char> <char>
#> 1: NA NA NA <NA> G02001876 Palbociclib
#> 2: NA NA NA <NA> G02001876 Palbociclib
#> 3: NA NA NA <NA> G02001876 Palbociclib
#> 4: NA NA NA <NA> G02001876 Palbociclib
#> 5: NA NA NA <NA> G02967907 GDC-0077
#> 6: NA NA NA <NA> G02967907 GDC-0077
#> 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: PI3K-A <NA> <NA> <NA> <NA> <NA>
#> 6: PI3K-A <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 CL130742 T-47D Breast T-47D unknown
#> 3: 168 CL131873 HCC1428 Breast HCC1428 unknown
#> 4: 168 CL131903 BT-483 Breast BT-483 unknown
#> 5: 168 CL130218 BT-474 Breast BT-474 unknown
#> 6: 168 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 drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
#> <char> <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 x
#> <char> <char> <char> <num> <lgcl>
#> 1: Breast MCF-7 unknown 30 NA
#> 2: Breast T-47D unknown 60 NA
#> 3: Breast HCC1428 unknown 74 NA
#> 4: Breast BT-483 unknown 130 NA
#> 5: Breast BT-474 unknown 70 NA
#> 6: Breast CAMA-1 unknown 53 NA
#>
#> $isobolograms
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
#> <char> <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 x
#> <char> <char> <char> <num> <lgcl>
#> 1: Breast MCF-7 unknown 30 NA
#> 2: Breast T-47D unknown 60 NA
#> 3: Breast HCC1428 unknown 74 NA
#> 4: Breast BT-483 unknown 130 NA
#> 5: Breast BT-474 unknown 70 NA
#> 6: Breast CAMA-1 unknown 53 NA
#>
#> $BlissScore
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2
#> <char> <num> <char> <char> <char> <char>
#> 1: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 2: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 3: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 4: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 5: <NA> NA G02967907 GDC-0077 PI3K-A <NA>
#> 6: <NA> NA G02967907 GDC-0077 PI3K-A <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 CL130742
#> 3: <NA> <NA> <NA> <NA> 168 CL131873
#> 4: <NA> <NA> <NA> <NA> 168 CL131903
#> 5: <NA> <NA> <NA> <NA> 168 CL130218
#> 6: <NA> <NA> <NA> <NA> 168 CL131438
#> i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char>
#> 1: MCF-7 Breast MCF-7 unknown
#> 2: T-47D Breast T-47D unknown
#> 3: HCC1428 Breast HCC1428 unknown
#> 4: BT-483 Breast BT-483 unknown
#> 5: BT-474 Breast BT-474 unknown
#> 6: CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $HSAScore
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2
#> <char> <num> <char> <char> <char> <char>
#> 1: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 2: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 3: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 4: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 5: <NA> NA G02967907 GDC-0077 PI3K-A <NA>
#> 6: <NA> NA G02967907 GDC-0077 PI3K-A <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 CL130742
#> 3: <NA> <NA> <NA> <NA> 168 CL131873
#> 4: <NA> <NA> <NA> <NA> 168 CL131903
#> 5: <NA> <NA> <NA> <NA> 168 CL130218
#> 6: <NA> <NA> <NA> <NA> 168 CL131438
#> i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char>
#> 1: MCF-7 Breast MCF-7 unknown
#> 2: T-47D Breast T-47D unknown
#> 3: HCC1428 Breast HCC1428 unknown
#> 4: BT-483 Breast BT-483 unknown
#> 5: BT-474 Breast BT-474 unknown
#> 6: CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $CIScore_50
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2
#> <char> <lgcl> <char> <char> <char> <char>
#> 1: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 2: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 3: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 4: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 5: <NA> NA G02967907 GDC-0077 PI3K-A <NA>
#> 6: <NA> NA G02967907 GDC-0077 PI3K-A <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 CL130742
#> 3: <NA> <NA> <NA> <NA> 168 CL131873
#> 4: <NA> <NA> <NA> <NA> 168 CL131903
#> 5: <NA> <NA> <NA> <NA> 168 CL130218
#> 6: <NA> <NA> <NA> <NA> 168 CL131438
#> i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char>
#> 1: MCF-7 Breast MCF-7 unknown
#> 2: T-47D Breast T-47D unknown
#> 3: HCC1428 Breast HCC1428 unknown
#> 4: BT-483 Breast BT-483 unknown
#> 5: BT-474 Breast BT-474 unknown
#> 6: CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $CIScore_80
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> normalization_type x i.Gnumber i.DrugName i.drug_moa i.Gnumber_2
#> <char> <lgcl> <char> <char> <char> <char>
#> 1: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 2: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 3: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 4: <NA> NA G02001876 Palbociclib CDK4|CDK6 <NA>
#> 5: <NA> NA G02967907 GDC-0077 PI3K-A <NA>
#> 6: <NA> NA G02967907 GDC-0077 PI3K-A <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 CL130742
#> 3: <NA> <NA> <NA> <NA> 168 CL131873
#> 4: <NA> <NA> <NA> <NA> 168 CL131903
#> 5: <NA> <NA> <NA> <NA> 168 CL130218
#> 6: <NA> <NA> <NA> <NA> 168 CL131438
#> i.CellLineName i.Tissue i.parental_identifier i.subtype
#> <char> <char> <char> <char>
#> 1: MCF-7 Breast MCF-7 unknown
#> 2: T-47D Breast T-47D unknown
#> 3: HCC1428 Breast HCC1428 unknown
#> 4: BT-483 Breast BT-483 unknown
#> 5: BT-474 Breast BT-474 unknown
#> 6: CAMA-1 Breast CAMA-1 unknown
#> i.ReferenceDivisionTime
#> <num>
#> 1: 30
#> 2: 60
#> 3: 74
#> 4: 130
#> 5: 70
#> 6: 53
#>
#> $Metrics
#> Key: <treatmentid, sampleid>
#> treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2
#> <char> <char> <char> <char> <char> <char> <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>
#> DrugName_3 Duration Gnumber Gnumber_2 CellLineName clid
#> <char> <num> <char> <char> <char> <char>
#> 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>
#> parental_identifier ReferenceDivisionTime subtype Tissue data_type
#> <char> <num> <char> <char> <char>
#> 1: <NA> NA <NA> <NA> single-agent
#> 2: <NA> NA <NA> <NA> single-agent
#> 3: <NA> NA <NA> <NA> single-agent
#> 4: <NA> NA <NA> <NA> single-agent
#> 5: <NA> NA <NA> <NA> single-agent
#> 6: <NA> NA <NA> <NA> single-agent
#> x_mean x_AOC x_AOC_range xc50 x_max ec50 x_inf
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.4766169 0.5233831 0.5685724 0.07649828 0.107050 0.06354470 0.08684205
#> 2: 0.6438030 0.3561970 0.3828886 0.26119890 0.281750 0.09897928 0.32080324
#> 3: 0.5797408 0.4202592 0.4560827 0.10802210 0.207125 0.08784832 0.21933259
#> 4: 0.4888085 0.5111915 0.5620006 0.06629065 0.111625 0.05911087 0.12311310
#> 5: 0.6458536 0.3541464 0.3770687 0.26781723 0.228300 0.13626047 0.27577126
#> 6: 0.4821213 0.5178787 0.5639825 0.06294109 0.148225 0.04029515 0.16592442
#> x_0 h r2 x_sd_avg fit_type
#> <num> <num> <num> <num> <char>
#> 1: 1 1.0283168 0.9853800 0.05272629 DRC3pHillFitModelFixS0
#> 2: 1 1.0574543 0.9465590 0.07259453 DRC3pHillFitModelFixS0
#> 3: 1 2.7932767 0.9787945 0.06655135 DRC3pHillFitModelFixS0
#> 4: 1 2.4657832 0.9946671 0.07915584 DRC3pHillFitModelFixS0
#> 5: 1 1.1867664 0.9616801 0.06463053 DRC3pHillFitModelFixS0
#> 6: 1 0.9041923 0.9740112 0.05594059 DRC3pHillFitModelFixS0
#> maxlog10Concentration N_conc normalization_type fit_source cotrt_value
#> <num> <int> <char> <char> <num>
#> 1: 1 10 RV gDR NA
#> 2: 1 10 RV gDR NA
#> 3: 1 10 RV gDR NA
#> 4: 1 10 RV gDR NA
#> 5: 1 10 RV gDR NA
#> 6: 1 10 RV gDR NA
#> source i.Gnumber i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2
#> <char> <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> G02001876 Palbociclib CDK4|CDK6 <NA> <NA>
#> 6: <NA> G02001876 Palbociclib CDK4|CDK6 <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 CL130218 BT-474
#> 3: <NA> <NA> <NA> 168 CL130742 T-47D
#> 4: <NA> <NA> <NA> 168 CL131438 CAMA-1
#> 5: <NA> <NA> <NA> 168 CL131873 HCC1428
#> 6: <NA> <NA> <NA> 168 CL131891 EFM-19
#> i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime
#> <char> <char> <char> <num>
#> 1: Breast MCF-7 unknown 30
#> 2: Breast BT-474 unknown 70
#> 3: Breast T-47D unknown 60
#> 4: Breast CAMA-1 unknown 53
#> 5: Breast HCC1428 unknown 74
#> 6: Breast EFM-19 unknown 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
#> drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 DrugName_3 Duration
#> <char> <char> <char> <char> <char> <char> <num>
#> 1: CDK4|CDK6 <NA> <NA> Palbociclib <NA> <NA> 168
#> 2: CDK4|CDK6 <NA> <NA> Palbociclib <NA> <NA> 168
#> 3: CDK4|CDK6 <NA> <NA> Palbociclib <NA> <NA> 168
#> Gnumber Gnumber_2 CellLineName clid parental_identifier
#> <char> <char> <char> <char> <char>
#> 1: G02001876 <NA> MCF-7 CL129757 MCF-7
#> 2: G02001876 <NA> BT-474 CL130218 BT-474
#> 3: G02001876 <NA> T-47D CL130742 T-47D
#> ReferenceDivisionTime subtype Tissue data_type x_mean x_AOC
#> <num> <char> <char> <char> <num> <num>
#> 1: 30 unknown Breast single-agent 0.4774514 0.5225486
#> 2: 70 unknown Breast single-agent 0.5916887 0.4083113
#> 3: 60 unknown Breast single-agent 0.5478704 0.4521296
#> x_AOC_range xc50 x_max ec50 x_inf x_0 h
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.5592516 0.1100133 -0.017025 0.1161741 -0.03117468 1 1.1100114
#> 2: 0.4338082 0.2091202 0.114275 0.1360264 0.16571556 1 0.9361851
#> 3: 0.4876840 0.1164343 0.111425 0.1033672 0.13053185 1 2.5415386
#> r2 x_sd_avg fit_type maxlog10Concentration N_conc
#> <num> <num> <char> <num> <int>
#> 1: 0.9880388 0.05887778 DRC3pHillFitModelFixS0 1 10
#> 2: 0.9555750 0.08197778 DRC3pHillFitModelFixS0 1 10
#> 3: 0.9815621 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 beta (2024-04-15 r86425)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.19-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_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [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_1.30.0 gDRimport_1.2.0
#> [3] PharmacoGx_3.8.0 CoreGx_2.8.0
#> [5] SummarizedExperiment_1.34.0 Biobase_2.64.0
#> [7] GenomicRanges_1.56.0 GenomeInfoDb_1.40.0
#> [9] IRanges_2.38.0 S4Vectors_0.42.0
#> [11] MatrixGenerics_1.16.0 matrixStats_1.3.0
#> [13] BiocGenerics_0.50.0
#>
#> 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_0.44.0 caTools_1.18.2
#> [16] utf8_1.2.4 promises_1.3.0 rmarkdown_2.26
#> [19] UCSC.utils_1.0.0 coop_0.6-3 xfun_0.43
#> [22] zlibbioc_1.50.0 cachem_1.0.8 jsonlite_1.8.8
#> [25] SnowballC_0.7.1 later_1.3.2 DelayedArray_0.30.0
#> [28] BiocParallel_1.38.0 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_3.60.0 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_1.12.0 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
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#> [100] mime_0.12