R/data.R

In koenvandenberge/traviz: Trajectory functions for visualization and interpretation.

#' A SlingshotDataset object, used for testing.
#'
#' This dataset contains the Slingshot trajectory from the data described in
#' Paul et al. (2015).
#'
#' @references
#' Franziska Paul, Yaara Arkin, Amir Giladi, DiegoAdhemar Jaitin, Ephraim Kenigsberg, Hadas KerenShaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen,
#' FeliciaKathrineBratt Lauridsen, Simon Haas, Andreas Schlitzer, Alexander Mildner, Florent Ginhoux,
#' Steen Jung, Andreas Trumpp, BoTorben Porse, Amos Tanay, and Ido Amit. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell, 163(7):1663–1677, 12 2015. ISSN 0092-
#' 8674. doi: 10.1016/J.CELL.2015.11.013. URL https://www.sciencedirect.com/science/article/
#' ii/S0092867415014932?via%3Dihub#app3.
#' @usage data("crv", package = "traviz")
"crv"

#' A count matrix, used for testing.
#'
#' This object contains the gene expression counts from the data described in
#' Paul et al. (2015).
#'
#' #' @references
#' Franziska Paul, Yaara Arkin, Amir Giladi, DiegoAdhemar Jaitin, Ephraim Kenigsberg, Hadas KerenShaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen,
#' FeliciaKathrineBratt Lauridsen, Simon Haas, Andreas Schlitzer, Alexander Mildner, Florent Ginhoux,
#' Steen Jung, Andreas Trumpp, BoTorben Porse, Amos Tanay, and Ido Amit. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell, 163(7):1663–1677, 12 2015. ISSN 0092-
#' 8674. doi: 10.1016/J.CELL.2015.11.013. URL https://www.sciencedirect.com/science/article/
#' ii/S0092867415014932?via%3Dihub#app3.
#' @usage data("counts", package = "traviz")
"counts"

#' A SingleCellExperiment object, used for testing.
#'
#' This object contains fitted smoothers using \code{tradeSeq}.
#'
#' #' @references
#' Franziska Paul, Yaara Arkin, Amir Giladi, DiegoAdhemar Jaitin, Ephraim Kenigsberg, Hadas KerenShaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen,
#' FeliciaKathrineBratt Lauridsen, Simon Haas, Andreas Schlitzer, Alexander Mildner, Florent Ginhoux,
#' Steen Jung, Andreas Trumpp, BoTorben Porse, Amos Tanay, and Ido Amit. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell, 163(7):1663–1677, 12 2015. ISSN 0092-
#' 8674. doi: 10.1016/J.CELL.2015.11.013. URL https://www.sciencedirect.com/science/article/
#' ii/S0092867415014932?via%3Dihub#app3.
#' @usage data("sce", package = "traviz")
"sce"