R/data.R

In robertamezquita/Inkwell: Containers for Curated Cell Type Signatures

#' Satija Lab Seurat Tutorial on PBMC 3k Markers
#'
#' The Satija lab published an online tutorial on the usage of Seurat using
#' a 3,000 cell PBMC dataset first published by 10X Genomics. Manual annotation
#' was performed on this dataset in the tutorial using the markers included herein.
#' 
#' @format `GeneSetCollection` class object consisting of the following genesets in
#' `GeneSet` class :
#'
#' * "CD4 T cells", "CD8 T cells", "B cells", "CD14+ Monocytes",
#'   "FCGR3A+ Monocytes", "NK cells", "Dendritic cells", "Megakaryocytes"
#'
#' @source <https://satijalab.org/seurat/pbmc3k_tutorial.html>
"pbmc3k_markers"

#' MCPcounter Defined Markers
#'
#' Becht. et al 2016 analyzed gene signatures from a plethora of data to define
#' conservative markers for major canonical cell types. 
#' 
#' @format `GeneSetCollection` class object consisting of the following genesets in
#' `GeneSet` class :
#'
#' * T cells; CD8 T cells; Cytotoxic lymphocytes; B lineage; NK cells;
#'   Monocytic lineage; Myeloid dendritic cells; Neutrophils;
#'   Endothelial cells; Fibroblasts"
#'
#' @source <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1070-5>
#' @source <https://github.com/ebecht/MCPcounter>
"MCPcounter_markers"