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Reference datasets for `singlepp`\n\n## Overview\n\nThis provides a number of prebuilt references for easy consumption by the [**singlepp**](https://github.com/LTLA/singlepp) library.\nIt is primarily based on the datasets available in the [**celldex**](https://bioconductor.org/packages/celldex) package,\nthemselves derived from the original [**SingleR**](https://bioconductor.org/packages/SingleR) publication.\nEach reference dataset is represented by four files that are described below.\n\n## File specification\n\n### `matrix.csv`\n\nThis is a CSV file containing a dense matrix of ranks for all samples.\nEach row corresponds to a sample where ranks are computed within each sample.\nWe store the ranks to avoid the need to store and transmit floating-point values.\nThis file does not contain any row or column names.\n\n### `genes.csv`\n\nThis is a CSV file containing information about each gene in `matrix.csv`.\nThe first column contains the Ensembl identifiers, the second column contains the gene symbols, and the third column contains Entrez IDs.\nMissing identifiers in any field are represented as empty strings.\nNo row or column names should be listed here.\n\n### `labels_*.csv`\n\nThis is a CSV file containing listing the label for each sample in `matrix.csv`.\nEach row corresponds to a column in `matrix.csv` and contains the label for the corresponding sample.\nNo row or column names should be listed here.\nEach `matrix.csv` may be associated with multiple label sets (e.g., broad or fine labels).\n\n### `markers_*.gmt`\n\nThis is a tab-delimited GMT file containing the ranked markers for each pairwise comparison between labels.\nOn each line, the first entry is label `X` and the second entry is label `Y`.\nThe remaining entries represent the row indices of markers defining `X` relative to `Y`.\nRow indices are 0-based and refer to the rows of `matrix.csv`.\nNote that indices are ranked, i.e., the strongest markers are listed first.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fsinglepp-references","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fsinglepp-references","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fsinglepp-references/lists"}