1. AnVILBilling::demo_rec
    a demonstration avReckoning object
    rda| rds
    avReckoning
  2. arrayMvout::afxsubDEG
    Multivariate outlier detection based on PCA of QA statistics
    json| rda| rds
    list
  3. arrayMvout::fig3map
    Multivariate outlier detection based on PCA of QA statistics
    json| rda| rds
    numeric
  4. arrayMvout::ilmQA
    Multivariate outlier detection based on PCA of QA statistics
    csv| json| rda| rds
    matrix|19 x 4
  5. arrayMvout::itnQA
    Multivariate outlier detection based on PCA of QA statistics
    csv| xlsx| json| ndjson| rda| rds
    data.frame|507 x 9
  6. arrayMvout::maqcQA
    Multivariate outlier detection based on PCA of QA statistics
    csv| xlsx| json| ndjson| rda| rds
    data.frame|120 x 11
  7. arrayMvout::s12cDEG
    Multivariate outlier detection based on PCA of QA statistics
    json| rda| rds
    list
  8. arrayMvout::spikQA
    Multivariate outlier detection based on PCA of QA statistics
    csv| xlsx| json| ndjson| rda| rds
    data.frame|12 x 9
  9. BiocFHIR::allin
    collection of synthea FHIR documents ingested
    json| rda| rds
    list
  10. BiocHail::kg_3202
    data.frame with metadata about 3202 samples genotyped against T2T reference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3202 x 22
  11. BiocHail::pcs_191k
    HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3202 x 5
  12. BiocHail::pcs_38k
    HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3202 x 8
  13. gwascat::ebicat_2020_04_30
    serialized gwaswloc instance from april 30 2020, sample of 50000 records
    rda| rds
    gwaswloc
  14. gwascat::efo.obo.g
    convert a typical OBO text file to a graphNEL instance (using Term elements)
    rda| rds
    graphNEL
  15. gwascat::g17SM
    SnpMatrix instance from chr17
    rda| rds
    SnpMatrix|90 x 89701
  16. gwascat::gg17N
    genotype matrix from chr17 1000 genomes
    csv| json| rda| rds
    matrix|90 x 87957
  17. gwascat::gr6.0_hg38
    image of locon6 in GRanges, lifted over to hg38
    rda| rds
    GRanges
  18. gwascat::gw6.rs_17
    character vector of rs numbers for SNP on chr17
    json| rda| rds
    character
  19. gwascat::gwastagger
    GRanges with LD information on 9998 SNP
    rda| rds
    GRanges
  20. gwascat::locon6
    location data for 10000 SNP
    csv| xlsx| json| ndjson| rda| rds
    data.frame|10000 x 3
  21. gwascat::low17
    SnpMatrix instance from chr17
    rda| rds
    SnpMatrix|60 x 196327
  22. gwascat::si.hs.37
    Seqinfo for GRCh37
    rda| rds
    Seqinfo
  23. gwascat::si.hs.38
    Seqinfo for GRCh38
    rda| rds
    Seqinfo
  24. hmdbQuery::hmdb1
    hmdb1: demonstration HMDB entry
    rda| rds
    HmdbEntry
  25. hmdbQuery::hmdb_disease
    hmdb_disease: Sept 2017 extract from hmdb.ca of direct disease associations
    rda| rds
    DataFrame
  26. hmdbQuery::hmdb_gene
    hmdb_gene: Sept 2017 extract from hmdb.ca of direct gene associations
    rda| rds
    DataFrame
  27. hmdbQuery::hmdb_omim
    hmdb_omim: Sept 2017 extract from hmdb.ca of direct omim associations
    rda| rds
    DataFrame
  28. hmdbQuery::hmdb_protein
    hmdb_protein: Sept 2017 extract from hmdb.ca of direct protein associations
    rda| rds
    DataFrame
  29. ivygapSE::ivySE
    ivySE: SummarizedExperiment for IvyGAP expression data and metadata
    rda| rds
    SummarizedExperiment
  30. keggorthology::KOgraph
    create a graph from a specific data frame format for KEGG orthology
    rda| rds
    graphNEL
  31. keggorthology::keggOrthDF
    create a graph from a specific data frame format for KEGG orthology
    csv| xlsx| json| ndjson| rda| rds
    data.frame|357 x 5
  32. ldblock::EUR_singletons
    singletons from EUR
    json| rda| rds
    character
  33. ldblock::sampinf_1kg
    population and relationship information for 1000 genomes
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3500 x 16
  34. MLInterfaces::brennan_2013_tabS7exc
    Clinical characterization of 158 GBM samples from https://doi.org/10.1016/j.cell.2013.09.034 supp table S7
    csv| xlsx| json| ndjson| rda| rds
    data.frame|158 x 16
  35. ontoProc::PROSYM
    PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
    csv| xlsx| json| ndjson| rda| rds
    data.frame|209947 x 2
  36. ontoProc::allGOterms
    allGOterms: data.frame with ids and terms
    csv| xlsx| json| ndjson| rda| rds
    data.frame|44541 x 2
  37. ontoProc::humrna
    humrna: a data.frame of SRA metadata related to RNA-seq in humans
    csv| xlsx| json| ndjson| rda| rds
    data.frame|513 x 12
  38. ontoProc::minicorpus
    minicorpus: a vector of annotation strings found in 'study title' of SRA metadata.
    json| rda| rds
    character
  39. ontoProc::packDesc2019
    packDesc2019: overview of ontoProc resources
    csv| xlsx| json| ndjson| rda| rds
    data.frame|13 x 8
  40. ontoProc::packDesc2021
    packDesc2021: overview of ontoProc resources
    csv| xlsx| json| ndjson| rda| rds
    data.frame|12 x 6
  41. ontoProc::packDesc2022
    packDesc2022: overview of ontoProc resources
    csv| xlsx| json| ndjson| rda| rds
    data.frame|14 x 7
  42. ontoProc::packDesc2023
    packDesc2023: overview of ontoProc resources
    csv| xlsx| json| ndjson| rda| rds
    data.frame|15 x 7
  43. ontoProc::stopWords
    stopWords: vector of stop words from xpo6.com
    json| rda| rds
    character
  44. parody::bushfire
    satellite data on bushfire scars
    csv| json| rda| rds
    matrix|38 x
  45. parody::tcost
    Data on milk transportation costs, from Johnson and Wichern, Applied Multivariate Statistical Analysis, 3rd edition
    csv| json| rda| rds
    matrix|36 x 3
  46. pogos::CCLE_drts
    compounds_v1: serialization of compounds info from PharmacoDb v1
    rda| rds
    DRTraceSet
  47. pogos::cell_lines_v1
    compounds_v1: serialization of compounds info from PharmacoDb v1
    rda| rds
    DFrame
  48. pogos::compounds_v1
    compounds_v1: serialization of compounds info from PharmacoDb v1
    rda| rds
    DFrame
  49. pogos::datasets_v1
    compounds_v1: serialization of compounds info from PharmacoDb v1
    rda| rds
    DFrame
  50. pogos::tissues_v1
    compounds_v1: serialization of compounds info from PharmacoDb v1
    rda| rds
    DFrame
  51. RbcBook1::bcr.cor
    Illustrative datasets for distance measures
    rda| rds
    dist
  52. RbcBook1::bcr.euc
    Illustrative datasets for distance measures
    rda| rds
    dist
  53. RbcBook1::bcr.kldist
    Illustrative datasets for distance measures
    rda| rds
    dist
  54. RbcBook1::bcr.man
    Illustrative datasets for distance measures
    rda| rds
    dist
  55. RbcBook1::bcr.mi
    Illustrative datasets for distance measures
    rda| rds
    dist
  56. RbcBook1::bcr.spear
    Illustrative datasets for distance measures
    rda| rds
    dist
  57. RbcBook1::bcr.tau
    Illustrative datasets for distance measures
    rda| rds
    dist
  58. RbcBook1::performance
    Results of tedious computations for computational inference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|100 x 4
  59. RbcBook1::performance
    Results of tedious computations for computational inference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|100 x 2
  60. RbcBook1::performance
    Results of tedious computations for computational inference
    csv| xlsx| json| ndjson| rda| rds
    data.frame|100 x 4
  61. scviR::clusters.adt
    ADT-based cluster labels for 7472 cells in OSCA chapter 12 analysis
    json| rda| rds
    factor
  62. scviR::clusters.rna
    mRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysis
    json| rda| rds
    factor
  63. ssrch::docset_cancer68
    DocSet instance with metadata from 68 cancer studies
    rda| rds
    DocSet
  64. ssrch::study_publ_dates
    publication dates for 6000 SRA transcriptome studies
    csv| xlsx| json| ndjson| rda| rds
    data.frame|6212 x 2
  65. ssrch::titles68
    titles for 68 cancer studies
    json| rda| rds
    character
  66. ssrch::urls68
    pubmed URLs for subset of 68 cancer studies
    json| rda| rds
    character
  67. tenXplore::CellTypes
    cellTypes: data.frame with ids and terms
    rda| rds
    TermSet
  68. tenXplore::tenx500
    tenx500: serialized full SummarizedExperiment for demonstration
    rda| rds
    SummarizedExperiment
  69. TFutils::cisbpTFcat
    cisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog
    csv| xlsx| json| ndjson| rda| rds
    data.frame|7592 x 28
  70. TFutils::cisbpTFcat_2.0
    cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749
    csv| xlsx| json| ndjson| rda| rds
    data.frame|5861 x 28
  71. TFutils::demo_fimo_granges
    a list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
    rda| rds
    list
  72. TFutils::encode690
    encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges
    rda| rds
    DFrame
  73. TFutils::fimo16
    fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs
    rda| rds
    GenomicFiles
  74. TFutils::fimoMap
    fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs
    csv| xlsx| json| ndjson| rda| rds
    data.frame|689 x 2
  75. TFutils::gwascat_hg19_chr17
    gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17
    rda| rds
    GRanges
  76. TFutils::hocomoco.mono
    hocomoco.mono: data.frame with information on HOCOMOCO TFs for human
    csv| xlsx| json| ndjson| rda| rds
    data.frame|771 x 9
  77. TFutils::hocomoco.mono.sep2018
    hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download
    csv| xlsx| json| ndjson| rda| rds
    data.frame|769 x 9
  78. TFutils::lambert_snps
    lambert_snps is Table S3 of Lambert et al PMID 29425488
    csv| xlsx| json| ndjson| rda| rds
    data.frame|143864 x 6
  79. TFutils::metadata_tf
    metadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files
    csv| json| rda| rds
    list
  80. TFutils::named_tf
    named_tf: named list with the names being the hgnc_symbol of the motif_id
    csv| json| rda| rds
    list
  81. TFutils::seqinfo_hg19_chr17
    a Seqinfo instance for a chr17 in hg19
    rda| rds
    Seqinfo
  82. TFutils::tfhash
    tfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ
    csv| xlsx| json| ndjson| rda| rds
    data.frame|164130 x 3
  83. TFutils::tftColl
    tftColl: GSEABase GeneSetCollection for transcription factor targets
    rda| rds
    GeneSetCollection
  84. TFutils::tftCollMap
    tftCollMap: data.frame with information on MSigDb TFs for human
    csv| xlsx| json| ndjson| rda| rds
    data.frame|615 x 3
  85. vtpnet::cancerMap
    variant-transcription factor-phenotype networks
    csv| xlsx| json| ndjson| rda| rds
    data.frame|50 x 2
  86. vtpnet::maurGWAS
    variant-transcription factor-phenotype networks
    rda| rds
    GRanges
  87. vtpnet::pax4
    variant-transcription factor-phenotype networks
    rda| rds
    GRanges
  88. vtpnet::pax4_75
    variant-transcription factor-phenotype networks
    rda| rds
    GRanges
  89. vtpnet::pax4_85
    variant-transcription factor-phenotype networks
    rda| rds
    GRanges
  90. xenLite::e79sym
    mapping from ENSG to symbols based on EnsDb.Hsapiens.v79
    json| rda| rds
    character