1. DaMiRseq::SE
    Example gene-expression dataset for DaMiRseq package
    rda| rds
    SummarizedExperiment
  2. DaMiRseq::SEtest_norm
    A sample dataset with a normalized count matrix for "testthat" functions.
    rda| rds
    SummarizedExperiment
  3. DaMiRseq::data_min
    Example gene-expression dataset for DaMiRseq package
    csv| xlsx| json| ndjson| rda| rds
    data.frame|40 x 87
  4. DaMiRseq::data_norm
    A dataset with a normalized matrix to test several DaMiRseq functions: sample data are a subset of Genotype-Tissue Expression (GTEx) RNA-Seq database (dbGap Study Accession: phs000424.v6.p1)
    rda| rds
    SummarizedExperiment
  5. DaMiRseq::data_reduced
    Example gene-expression dataset for DaMiRseq package
    csv| xlsx| json| ndjson| rda| rds
    data.frame|40 x 138
  6. DaMiRseq::data_relief
    Example ranking dataset for DaMiRseq package
    csv| xlsx| json| ndjson| rda| rds
    data.frame|87 x 2
  7. DaMiRseq::df
    Example gene-expression dataset for DaMiRseq package
    rda| rds
    DFrame
  8. DaMiRseq::selected_features
    Example gene-expression dataset for DaMiRseq package
    csv| xlsx| json| ndjson| rda| rds
    data.frame|40 x 7
  9. DaMiRseq::sv
    Example Surrogate Variables dataset for DaMiRseq package
    csv| json| rda| rds
    matrix|40 x
  10. PIUMA::df_test_proj
    A dataset to test the 'dfToProjection' and 'dfToDistance' funtions of 'PIUMA' package.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|30 x 2
  11. PIUMA::tda_test_data
    A TDAobj to test the 'PIUMA' package.
    rda| rds
    TDAobj
  12. PIUMA::vascEC_meta
    Example datasets for PIUMA package
    csv| xlsx| json| ndjson| rda| rds
    data.frame|1180 x 2
  13. PIUMA::vascEC_norm
    We tested PIUMA on a subset of the single-cell RNA Sequencing dataset (GSE:GSE193346 generated and published by Feng et al. (2022) on Nature Communication to demonstrate that distinct transcriptional profiles are present in specific cell types of each heart chambers, which were attributed to have roles in cardiac development. In this tutorial, our aim will be to exploit PIUMA for identifying sub-population of vascular endothelial cells, which can be associated with specific heart developmental stages. The original dataset consisted of three layers of heterogeneity: cell type, stage and zone (i.e., heart chamber). Our testing dataset was obtained by subsetting vascular endothelial cells (cell type) by Seurat object, extracting raw counts and metadata. Thus, we filtered low expressed genes and normalized data by DaMiRseq
    csv| json| rda| rds
    matrix|1180 x 838