- consensusOV::GSE14764.esetSample ExpressionSet from MetaGxOvarian
- CoreGx::clevelandSmall_cSetCleaveland_mut RadioSet subsetted and cast as CoreSet
- CoreGx::exampleDataMapperExample LongTableDataMapper
- CoreGx::merckLongTableMerck Drug Combination Data LongTable
- CoreGx::nci_TRE_smallNCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset
- CREAM::COREs
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- genefu::annot.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::annot.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::annot.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::claudinLowDataclaudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.
- genefu::data.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::data.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::data.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::demo.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::demo.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::demo.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::mod1Gene modules published in Desmedt et al. 2008
- genefu::mod2Gene modules published in Wirapati et al. 2008
- genefu::modelOvcAngiogenicModel used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.
- genefu::pam50PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::pam50.robustPAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::pam50.scalePAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::scmgene.robustSubtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
- genefu::scmod1.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
- genefu::scmod2.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
- genefu::sig.endoPredictSignature used to compute the endoPredict signature as published by Filipits et al 2011
- genefu::sig.gene70Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
- genefu::sig.gene76Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005
- genefu::sig.geniusGene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.
- genefu::sig.ggiGene expression Grade Index (GGI) as published in Sotiriou et al. 2006
- genefu::sig.oncotypedxSignature used to compute the OncotypeDX signature as published by Paik et al 2004
- genefu::sig.pik3cagsGene expression Grade Index (GGI) as published in Sotiriou et al. 2006
- genefu::sig.tamr13Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.
- genefu::sigOvcAngiogenicsigOvcAngiogenic dataset
- genefu::sigOvcCrijnssigOvcCrijns dataset
- genefu::sigOvcSpentzossigOcvSpentzos dataset
- genefu::sigOvcTCGAsigOvcTCGA dataset
- genefu::sigOvcYoshiharasigOvcYoshihara dataset
- genefu::ssp2003SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2003.robustSSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2003.scaleSSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2006SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- genefu::ssp2006.robustSSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- genefu::ssp2006.scaleSSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- MM2Sdata::GSE36594ExprNormalized gene expression data for Mouse MB samples (from GSE36594).
- MM2Sdata::GSE37418ExprNormalized gene expression data for Human MB (GSE37418).
- mRMRe::cgps.annotPart of the large pharmacogenomic dataset published by Garnett et al. within the Cancer Genome Project (CGP)
- mRMRe::cgps.gePart of the large pharmacogenomic dataset published by Garnett et al. within the Cancer Genome Project (CGP)
- mRMRe::cgps.ic50Part of the large pharmacogenomic dataset published by Garnett et al. within the Cancer Genome Project (CGP)
- PDATK::CSPC_MAEA 'MultiAssayExperiment' containing cohorts of pancreatic cancer patients, for use in package examples.
- PDATK::birnbaumPublished classifier gene signature for Birnbaum
- PDATK::chenPublished classifier gene signature for Chen
- PDATK::cohortSubtypeDFsA list of sample subtypes for the data in sampleCohortList
- PDATK::haiderSigScoresClassifier survival scores for Haider
- PDATK::sampleClinicalModelSample ClinicalModel Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleCohortListA Set of Example Patient Cohorts
- PDATK::sampleICGCmicroA Sample SurvivalExperiment Containing Data from the ICGC micro-array cohort from 'MetaGxPancreas'
- PDATK::samplePCOSPmodelA Sample PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::samplePCOSPpredListSample CohortList with PCOSP Risk Predictions
- PDATK::samplePCSIsurvExpSample SurvivalExperiment Containing the PCSI rna-sequencing cohort from 'MetaGxPancreas'.
- PDATK::sampleRGAmodelSample RGA Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleRLSmodelSample RLS Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleTrainedPCOSPmodelA Sample Trained PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleValPCOSPmodelSample Validated PCOSP Model for Plotting Examples
- PharmacoGx::CCLEsmallCancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
- PharmacoGx::CMAPsmallConnectivity Map Example PharmacoSet
- PharmacoGx::GDSCsmallGenomics of Drug Sensitivity in Cancer Example PharmacoSet
- PharmacoGx::HDAC_genesHDAC Gene Signature
- survcomp::mainz7gSubset of MAINZ dataset containing gene expression, annotations and clinical data.
- survcomp::nki7gSubset of NKI dataset containing gene expression, annotations and clinical data.
- survcomp::transbig7gSubset of the TRANSBIG dataset containing gene expression, annotations and clinical data.
- survcomp::unt7gSubset of UNT dataset containing gene expression, annotations and clinical data.
- survcomp::upp7gSubset of UPP dataset containing gene expression, annotations and clinical data.
- survcomp::vdx7gSubset of VDX dataset containing gene expression, annotations and clinical data.
- ToxicoGx::HCC_sigHCC_sig dataset
- ToxicoGx::TGGATESsmallTGGATESsmall dataset
- Xeva::PDXMIPDX-MI data
- Xeva::brcaPDXE breast cancer dataset
- Xeva::repdxExample PDX dataset
