Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

Analysis of Large-Scale Pharmacogenomic Data

c(
    person(given="Petr", family="Smirnov", email="petr.smirnov@uhnresearch.ca",
        role=c("aut")),
    person(given="Christopher", family="Eeles",
        email="christopher.eeles@uhnresearch.ca", role=c("aut")),
    person(given="Zhaleh", family="Safikhani", role=c("aut")),
    person(given="Mark", family="Freeman", role=c("aut")),
    person(given="Feifei", family="Li", email="ff.li@mail.utoronto.ca", role=c("aut")),
    person("Benjamin", "Haibe-Kains", email="benjamin.haibe.kains@utoronto.ca", role=c("aut", "cre"))
    )

Contains a set of functions to perform large-scale analysis of
    pharmaco-genomic data. These include the PharmacoSet object for storing
    the results of pharmacogenomic experiments, as well as a number of functions
    for computing common summaries of drug-dose response and correlating them
    with the molecular features in a cancer cell-line.

pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown, BiocStyle, R.utils

BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, magicaxis,
RColorBrewer, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
checkmate, boot, coop

GeneExpression, Pharmacogenetics, Pharmacogenomics,
Software, Classification

'GR.R' 'GWC.R' 'PharmacoSet-class.R' 'PharmacoSet-accessors.R'
'PharmacoSet-utils.R' 'RcppExports.R' 'adaptiveMatthewCor.R'
'callingWaterfall.R' 'class-SignatureClass.R' 'computeABC.R'
'computeAUC.R' 'computeAUC_old.R' 'computeAmax.R'
'computeDSS.R' 'computeDrugSensitivity.R' 'computeGR.R'
'computeIC50.R' 'computeICn.R' 'computeSlope.R'
'computeSynergy.R' 'connectivityScore.R' 'cosinePerm.R'
'datasets.R' 'downloadPSet.R' 'downloadSignatures.R'
'drugDoseResponseCurve.R' 'drugPerturbationSig.R'
'filterNoisyCurves.R' 'geneDrugPerturbation.R'
'geneDrugSensitivity.R' 'geneDrugSensitivityPBCorr.R'
'geneDrugSensitivityPCorr.R' 'getRawSensitivityMatrix.R'
'globals.R' 'intersectPSets.R' 'logLogisticRegression.R'
'matthewCor.R' 'mergePSets.R' 'methods-[.R'
'methods-drugSensitivitySig.R' 'methods-intersect.R'
'methods-subsetTo.R' 'methods-summarizeMolecularProfiles.R'
'methods-summarizeSensitivityProfiles.R' 'plotPSig.R'
'rankGeneDrugPerturbation.R' 'rankGeneDrugSensitivity.R'
'sanityCheck.R' 'updateObject-methods.R' 'zzz.R'