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- BreedingExperiment::demoBreedingA demonstration breeding population
- CDEnrich::cd_GenesetsCurated Cell Death Pathway Gene Sets
- CDEnrich::demo_all_genesDemonstration Background Gene Universe
- CDEnrich::demo_degDemonstration DEG List for Single-Group ORA
- CDEnrich::demo_deg_listDemonstration DEG Lists for Multi-Group ORA
- CDEnrich::demo_exprDemonstration Expression Matrix for ssGSEA
- CDEnrich::demo_groupDemonstration Sample Groups for ssGSEA
- CDEnrich::demo_rank_apopDemonstration Ranked Gene List for Single-Group GSEA
- CDEnrich::demo_rank_apop_listDemonstration Ranked Gene Lists for Multi-Group GSEA
- CDEnrich::demo_targeted_degDemonstration DEG List for Targeted ORA
- CDEnrich::representative_genesRepresentative Gene Sets for Cell Death Types
- CDEnrich::representative_pathwaysRepresentative Pathway Recommendation Metadata
- DEP::DiUbiDiUbi - Ubiquitin interactors for different diubiquitin-linkages (UbIA-MS dataset)
- DEP::DiUbi_ExpDesignExperimental design of the DiUbi dataset
- DEP::UbiLengthUbiLength - Ubiquitin interactors of different linear ubiquitin lengths (UbIA-MS dataset)
- DEP::UbiLength_ExpDesignExperimental design of the UbiLength dataset
- ECLIPSE::post_qc_contigsExample Post-QC TCR contigs that would be generated within ECLIPSE and passed to findThreeChainClones.
- ECLIPSE::test_seuratExample minimal Seurat object without TCR information.
- ECLIPSE::test_seurat_with_tcrExample Seurat object with TCR information generated by running the ECLIPSE function.
- ECLIPSE::vignette_objectExample small Seurat object without TCR information.
- epiPortrait::example_seExample Epigenetic Portrait Dataset
- epiwraps::exampleDNAmeExample DNAme data on some active gene bodies
- epiwraps::exampleESEExample EnrichmentSE object
- epiwraps::geneBodiesExample DNAme data on some active gene bodies
- GeneSCARAB::circa_table_genescarabcirca_table_genescarab
- ggwas::example_gwasExample GWAS dataset
- hmagmaR::annotated_genesExample microglia PLAC-seq dataset
- hmagmaR::enhancerRegionsExample microglia PLAC-seq dataset
- hmagmaR::gwasExample microglia PLAC-seq dataset
- hmagmaR::hicExample microglia PLAC-seq dataset
- hmagmaR::promoterRegionsExample microglia PLAC-seq dataset
- hmagmaR::regulatoryRegionsExample microglia PLAC-seq dataset
- hmagmaR::snpgeneexonExample microglia PLAC-seq dataset
- hmagmaR::snpsExample microglia PLAC-seq dataset
- IntegratedLearner::Franzosa_MAE_trainFranzosa multiclass MAE training fixture
- IntegratedLearner::Franzosa_MAE_validFranzosa multiclass MAE validation fixture
- IntegratedLearner::FranzosaE_2019_CuratedMetabolomeFranzosa et al. 2019 training metabolome table
- IntegratedLearner::FranzosaE_2019_CuratedMetadataFranzosa et al. 2019 training metadata
- IntegratedLearner::FranzosaE_2019_CuratedSpeciesProfileFranzosa et al. 2019 training species profile
- IntegratedLearner::FranzosaE_2019_Validation_CuratedMetabolomeFranzosa et al. 2019 validation metabolome table
- IntegratedLearner::FranzosaE_2019_Validation_CuratedMetadataFranzosa et al. 2019 validation metadata
- IntegratedLearner::FranzosaE_2019_Validation_CuratedSpeciesProfileFranzosa et al. 2019 validation species profile
- IntegratedLearner::gene_allTCGA BRCA gene-level table
- IntegratedLearner::mir_allTCGA BRCA microRNA-level table
- IntegratedLearner::NLIBDNLIBD binary-outcome PCL fixture
- IntegratedLearner::NLIBD_MAENLIBD binary-outcome MAE fixture
- IntegratedLearner::pregnancyPregnancy continuous-outcome PCL fixture
- IntegratedLearner::pregnancy_MAEPregnancy continuous-outcome MAE fixture
- IntegratedLearner::PRISMPRISM binary-outcome PCL fixture
- IntegratedLearner::PRISM_MAEPRISM binary-outcome MAE fixture
- IntegratedLearner::TCGA_survival_MAE_trainTCGA BRCA survival MAE training fixture
- IntegratedLearner::TCGA_survival_MAE_validTCGA BRCA survival MAE validation fixture
- KODAMA::lymphomaLymphoma gene-expression data
- KODAMA::MetRefNuclear Magnetic Resonance spectra of urine samples
- KODAMA::USAState of the Union data
- LongOmicsTraj::lot_glucoldCleaned longitudinal transcriptomics dataset from the GLUCOLD study
- LongOmicsTraj::lot_glucold_clinicalGLUCOLD clinical metadata
- LongOmicsTraj::lot_glucold_expressionGLUCOLD expression matrix
- LongOmicsTraj::lot_glucold_otsGLUCOLD LongOmicsTraj object with OTS results
- loopcityData::GM12878_10KbLoops
- loopcityData::GM12878_10KbLoopsChr21
- MagellanNTK::lldatalldata dataset
- MagellanNTK::lldata1lldata1 dataset
- MagellanNTK::lldata12lldata12 dataset
- MagellanNTK::lldata123lldata123 dataset
- mesa::BSgenome.Hsapiens.NCBI.GRCh38.CpG.distributionPre-calculated CpG distribution values for BSgenomes
- mesa::BSgenome.Hsapiens.UCSC.hg19.CpG.distributionPre-calculated CpG distribution values for BSgenomes
- mesa::BSgenome.Mmusculus.UCSC.mm10.CpG.distributionPre-calculated CpG distribution values for BSgenomes
- mesa::ENCODEbadRegions2019 ENCODE list of poorly mapped regions in hg38
- mesa::exampleMouseA small example qseaSet with 5 paired tumour/normal samples.
- mesa::exampleTumourNormalA small example qseaSet with 5 paired tumour/normal samples.
- mesa::FantomRegionsFANTOM5 regions for GRCh38
- mesa::gc_hg38_1000kbGC content across the human genome (hg38/GRCh38)
- mesa::gc_hg38_500kbGC content across the human genome (hg38/GRCh38)
- mesa::gc_hg38_50kbGC content across the human genome (hg38/GRCh38)
- mesa::hg19ToHg38.over.chainhg19tohg38 liftover chain
- mesa::hg38_450kArrayGRInfinium 450k probe locations for hg38.
- mesa::hg38CpGIslandsCpG islands for hg38.
- mesa::hg38UltraStableProbesUltra-stable methylated regions (GRCh38)
- mesa::map_hg38_1000kbMappability across the human genome (hg38/GRCh38)
- mesa::map_hg38_500kbMappability across the human genome (hg38/GRCh38)
- mesa::map_hg38_50kbMappability across the human genome (hg38/GRCh38)
- mgcca::X1Simulated cardiovascular multi-table example data
- mgcca::X2Simulated cardiovascular multi-table example data
- mgcca::X3Simulated cardiovascular multi-table example data
- MiCARA::example_metadataSynthetic Example Sample Metadata
- MiCARA::example_pathwaysSynthetic Example Functional Pathways Matrix
- MiCARA::example_taxaSynthetic Example Taxa Abundance Matrix
- MOTL::LrnLearning dataset
- MOTL::TL_paramTransfer learning parameters
- MOTL::TrgTarget datasets
- NADIA::nadia_diaExample DIA experiment, already preprocessed
- OmniCorr::metadataMetadata information
- OmniCorr::MetagenomicsExample Metagenomics dataset
- OmniCorr::MetatranscriptomicsExample Metatranscriptomics dataset
- OmniCorr::TranscriptomicsExample Transcriptomics dataset
- path2path::demo_pathwaysSynthetic demonstration pathway collection
- path2path::demo_zSynthetic demonstration input matrix
- pdactrace::atlas_metadataAtlas metadata
- pdactrace::default_templatesDefault trajectory templates (12-template catalog, v0.4.0)
- pdactrace::meta_analysisRandom-effects meta-analysis table
- pdactrace::pdactrace_data_sourcesPublic-data accession table backing list_data_sources()
- pdactrace::pdactrace_external_anchorsExternal PDAC biomarker anchor provenance table
- pdactrace::pdactrace_protein_betasPer-stage tissue-protein effect-size table for trajectory plotting
- pdactrace::pdactrace_referencepdactrace reference DB schema (v0.4.0, 12-template catalog with Early × 4 surface)
- pdactrace::toy_coldataSynthetic stage / cohort metadata for runnable examples
- pdactrace::toy_countsSynthetic RNA count matrix for runnable examples
- pdactrace::toy_proteinSynthetic tissue-protein log2 intensity matrix for runnable examples
- postexportKinetics::postexport_exampleSmall synthetic example dataset
- postexportKinetics::postexport_example_truthSimulation truth for the example dataset
- prolfqua::data_checksummarizationrobust87Reference input for the robust summarisation check (87 percent)
- prolfqua::data_checksummarizerobust69Reference input for the robust summarisation check (69 percent)
- prolfqua::data_ionstarIonStar peptide-level example data
- prolfqua::x5463yzwer453bbbFactor annotation of 36 samples
- Protein2Tissue::ee_tbHuman Protein Atlas tissue expression database
- Protein2Tissue::plasma_dataExample plasma proteomics dataset of age-associated protein expression
- Protein2Tissue::tissue_mapAn example of the data frame the for the 'tissue_groups' parameter of 'geneClassification'.
- RAMEN::test_covariatesConcomitant variable example data set
- RAMEN::test_environmental_matrixEnvironmental exposures example data set
- RAMEN::test_genotype_informationGenotype metadata example data set
- RAMEN::test_genotype_matrixGenotype matrix example
- RAMEN::test_methylation_dataMethylation data matrix example
- RAMEN::ultrastable_cpgsUltrastable probes
- reglScatterplotR::reglScatterExampleExample single-cell UMAP embedding
- RPBC::haley_gbm_exampleHaley GBM IMC Example Dataset
- sbivar::VicariSpatial transcriptomics and metabolomics data of mouse brain
- sceptre::gene_position_data_frame_grch37Gene position data frames
- sceptre::gene_position_data_frame_grch38Gene position data frames
- sceptre::grna_target_data_frame_highmoigRNA target data frame
- sceptre::highmoi_example_dataExample high-MOI data
- sceptre::lowmoi_example_dataExample low-MOI data
- scOverlay::sce_mpnst_exampleExample MPNST SingleCellExperiment for the scOverlay vignette
- scOverlay::sce_overlay_exampleSmall example SingleCellExperiment for scOverlay
- scProkaR::sce1Example bacterial single-cell dataset
- scSimEval::example_batch_infoExample Batch Annotations Vector
- scSimEval::example_cell_typesExample Cell-Type Annotations Vector
- scSimEval::example_multiomicsSynthetic Example Multiomics Benchmarking Dataset
- scSimEval::example_scatacSynthetic Example scATAC-seq Benchmarking Dataset
- scSimEval::example_scrnaSynthetic Example scRNA-seq Benchmarking Dataset
- selexprepR::selexprep_public_catalogCurated public HT-SELEX catalog
- SpaMTP::adduct_fileCommon adduct constants
- SpaMTP::reaction_typePathway-network reaction styles
- SwitchClass::CRC_subsetCRC subset data
- tTEscanR::default_tTEscanR_metadataMetadata of mRNA and tRNA data
- tTEscanR::default_tTEscanR_mRNA_datamRNA Expression Data Subset
- tTEscanR::default_tTEscanR_tRNA_datatRNA Expression Data Subset
- WithinHostExperiment::example_wheExample WithinHostExperiment dataset
- woven::woven_exampleExample dataset for WOVEN
