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- AnVILBilling::demo_reca demonstration avReckoning object
- arrayMvout::afxsubDEGMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::fig3mapMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::ilmQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::itnQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::maqcQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::s12cDEGMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::spikQAMultivariate outlier detection based on PCA of QA statistics
- BiocFHIR::allincollection of synthea FHIR documents ingested
- BiocHail::kg_3202data.frame with metadata about 3202 samples genotyped against T2T reference
- BiocHail::pcs_191kHWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
- BiocHail::pcs_38kHWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
- bronchialIL13::HAHdata on Affymetrix U133a chips regarding time course response of human bronchial cell line A549 to IL13
- bronchialIL13::HAHrmadata on Affymetrix U133a chips regarding time course response of human bronchial cell line A549 to IL13
- dressCheck::c119an N=119 expression set based on CEL files from JCO.zip
- dressCheck::corrpDressman's RMA+SFR corrected quantifications for 116 ovarian cancer samples
- dressCheck::corrp116Dressman's RMA+SFR corrected quantifications for 116 ovarian cancer samples
- dressCheck::DrAsGivenQuantifications of 119 ovarian cancer samples as distributed at Duke's platinum.php
- dressCheck::E2F3sig.probesAffymetrix probe identifiers for the E2F3 pathway signature of Bild et al.
- dressCheck::e2f3WtsCoefficients to weight components of E2F3 pathway to score for activity, derived from SVD applied to Bild's data
- dressCheck::platsigprobesaffymetrix probe identifiers for the platinum responsiveness signature
- dressCheck::pwLinesA representation of Bild's HMEC lines for pathway signature identification
- dressCheck::Src.probesAffymetrix probe identifiers for the Src pathway signature of Bild et al.
- dressCheck::srcWtsCoefficients to weight components of Src pathway to score for activity, derived from SVD applied to Bild's data
- gaschYHS::fig3Data from PMID 11102521, Transcriptional responses of yeast to environmental stress, A Gasch and colleagues (2001)
- gaschYHS::gaschYHSData from PMID 11102521, Transcriptional responses of yeast to environmental stress, A Gasch and colleagues (2001)
- golubEsets::Golub_MergeCombined Test and Training Sets from the Golub Paper
- golubEsets::Golub_TestTest Set Data from the Golub Paper
- golubEsets::Golub_TrainTraining Set from the Golub Paper
- golubEsets::golubMergeCombined Test and Training Sets from the Golub Paper
- golubEsets::golubTestTest Set Data from the Golub Paper
- golubEsets::golubTrainTraining Set from the Golub Paper
- gwascat::ebicat_2020_04_30serialized gwaswloc instance from april 30 2020, sample of 50000 records
- gwascat::efo.obo.gconvert a typical OBO text file to a graphNEL instance (using Term elements)
- gwascat::g17SMSnpMatrix instance from chr17
- gwascat::gg17Ngenotype matrix from chr17 1000 genomes
- gwascat::gr6.0_hg38image of locon6 in GRanges, lifted over to hg38
- gwascat::gw6.rs_17character vector of rs numbers for SNP on chr17
- gwascat::gwastaggerGRanges with LD information on 9998 SNP
- gwascat::locon6location data for 10000 SNP
- gwascat::low17SnpMatrix instance from chr17
- gwascat::si.hs.37Seqinfo for GRCh37
- gwascat::si.hs.38Seqinfo for GRCh38
- harbChIP::harbChIPExperimental Data Package: harbChIP
- harbChIP::sceUpstrBiostrings representations of S. cerevisiae upstream regions
- ivygapSE::ivySEivySE: SummarizedExperiment for IvyGAP expression data and metadata
- Iyer517::Iyer517exprSet instance Iyer517, time series on transcriptional response of fibroblasts to serum
- Iyer517::Iyer517GOPartly annotated version of Iyer517 data
- Iyer517::IyerAnnotatedPartly annotated version of Iyer517 data
- keggorthology::keggOrthDFcreate a graph from a specific data frame format for KEGG orthology
- keggorthology::KOgraphcreate a graph from a specific data frame format for KEGG orthology
- ldblock::EUR_singletonssingletons from EUR
- ldblock::sampinf_1kgpopulation and relationship information for 1000 genomes
- leeBamViews::leeRPKMsupplemental data extract on RNA seq results in yeast
- leeBamViews::leeUnnsupplemental data extracts on existing evidence of transcription in yeast
- MAQCsubset::afxsubExperimental Data Package: MAQCsubset
- MAQCsubset::afxsubRMAExperimental Data Package: MAQCsubset
- MAQCsubset::afxsubRMAESExperimental Data Package: MAQCsubset
- MAQCsubset::gehMAQCsubDefExcerpt from GE Codelink array contributions to MAQC
- MAQCsubset::gehSubRawExcerpt from GE Codelink array contributions to MAQC
- MAQCsubset::gnfCerebHiGene lists for hi or low abundance in cerebellum according to Novartis GNF symatlas
- MAQCsubset::gnfCerebLowGene lists for hi or low abundance in cerebellum according to Novartis GNF symatlas
- MAQCsubset::ilmMAQCsubRExperimental Data Package: MAQCsubset
- MLInterfaces::brennan_2013_tabS7excClinical characterization of 158 GBM samples from https://doi.org/10.1016/j.cell.2013.09.034 supp table S7
- mvoutData::ILM1raw expression data for evaluation of outlier detection algorithms
- mvoutData::s12craw expression data for evaluation of outlier detection algorithms
- Neve2006::neveCGHmatchNeve Cancer Cell 2006 expression plus CGH data
- Neve2006::neveExCGHNeve Cancer Cell 2006 expression plus CGH data
- Neve2006::neveRMAmatchNeve Cancer Cell 2006 expression plus CGH data
- ontoProc::allGOtermsallGOterms: data.frame with ids and terms
- ontoProc::humrnahumrna: a data.frame of SRA metadata related to RNA-seq in humans
- ontoProc::minicorpusminicorpus: a vector of annotation strings found in 'study title' of SRA metadata.
- ontoProc::packDesc2019packDesc2019: overview of ontoProc resources
- ontoProc::packDesc2021packDesc2021: overview of ontoProc resources
- ontoProc::packDesc2022packDesc2022: overview of ontoProc resources
- ontoProc::packDesc2023packDesc2023: overview of ontoProc resources
- ontoProc::PROSYMPROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
- ontoProc::stopWordsstopWords: vector of stop words from xpo6.com
- ontoProc2::cn2taga named vector with mapping from cell type phrase to CURIE for CL.owl
- ontoProc2::ncit_mapa named vector with values rdfs labels in NCI thesaurus, and names the corresponding formal ontology tags
- ontoProc2::tag2cna named vector with mapping from CURIE to cell type phrase for CL.owl
- parody::bushfiresatellite data on bushfire scars
- parody::tcostData on milk transportation costs, from Johnson and Wichern, Applied Multivariate Statistical Analysis, 3rd edition
- PlinkMatrix::example_GRangessample GRanges coordinated with example_PlinkMatrix
- PlinkMatrix::g445samplessample characteristics of 445 GEUVADIS samples
- pogos::CCLE_drtscompounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::cell_lines_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::compounds_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::datasets_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::tissues_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- RbcBook1::bcr.corIllustrative datasets for distance measures
- RbcBook1::bcr.eucIllustrative datasets for distance measures
- RbcBook1::bcr.kldistIllustrative datasets for distance measures
- RbcBook1::bcr.manIllustrative datasets for distance measures
- RbcBook1::bcr.miIllustrative datasets for distance measures
- RbcBook1::bcr.spearIllustrative datasets for distance measures
- RbcBook1::bcr.tauIllustrative datasets for distance measures
- RbcBook1::performanceResults of tedious computations for computational inference
- RbcBook1::performanceResults of tedious computations for computational inference
- RbcBook1::performanceResults of tedious computations for computational inference
- ssrch::docset_cancer68DocSet instance with metadata from 68 cancer studies
- ssrch::study_publ_datespublication dates for 6000 SRA transcriptome studies
- ssrch::titles68titles for 68 cancer studies
- ssrch::urls68pubmed URLs for subset of 68 cancer studies
- tenXplore::CellTypescellTypes: data.frame with ids and terms
- tenXplore::tenx500tenx500: serialized full SummarizedExperiment for demonstration
- TFutils::cisbpTFcatcisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog
- TFutils::cisbpTFcat_2.0cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749
- TFutils::demo_fimo_grangesa list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
- TFutils::encode690encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges
- TFutils::fimo16fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs
- TFutils::fimoMapfimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs
- TFutils::gwascat_hg19_chr17gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17
- TFutils::hocomoco.monohocomoco.mono: data.frame with information on HOCOMOCO TFs for human
- TFutils::hocomoco.mono.sep2018hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download
- TFutils::lambert_snpslambert_snps is Table S3 of Lambert et al PMID 29425488
- TFutils::metadata_tfmetadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files
- TFutils::named_tfnamed_tf: named list with the names being the hgnc_symbol of the motif_id
- TFutils::seqinfo_hg19_chr17a Seqinfo instance for a chr17 in hg19
- TFutils::tfhashtfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ
- TFutils::tftColltftColl: GSEABase GeneSetCollection for transcription factor targets
- TFutils::tftCollMaptftCollMap: data.frame with information on MSigDb TFs for human
- vtpnet::cancerMapvariant-transcription factor-phenotype networks
- vtpnet::maurGWASvariant-transcription factor-phenotype networks
- vtpnet::pax4variant-transcription factor-phenotype networks
- vtpnet::pax4_75variant-transcription factor-phenotype networks
- vtpnet::pax4_85variant-transcription factor-phenotype networks
- xenLite::e79symmapping from ENSG to symbols based on EnsDb.Hsapiens.v79