R/data.R

In wikiselev/clustools: Tools for cluster analysis of single cell high throughput data

#' Single cell RNA-Seq data extracted from a publication by Steven Quake.
#'
#' Source: Treutlein, B. et al. Reconstructing lineage hierarchies of the distal
#' lung epithelium using single-cell RNA-seq. Nature 509, 371–375 (2014).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52583}
#' 
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 50 cells and 5 clusters in this dataset.
"quake"

#' Single cell RNA-Seq data extracted from a publication by Sandberg.
#'
#' Source: Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals
#' dynamic, random monoallelic gene expression in mammalian cells. Science 343,
#' 193–196 (2014).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719}
#'
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 201 cells and 9 clusters in this dataset.
"sandberg"

#' Single cell RNA-Seq data extracted from a publication by Bernstein.
#'
#' Source: Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral
#' heterogeneity in primary glioblastoma. Science 344, 1396–1401 (2014).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57872}
#'
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 364 cells and 5 clusters in this dataset.
#' 
#' NOTE: This dataset is already processed with gene_filter1 and
#' log transformation.
"bernstein"

#' Single cell RNA-Seq data extracted from a publication by Linnarsson.
#'
#' Source: Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and
#' hippocampus revealed by single-cell RNA-seq. Science 347, 1138–1142 (2015).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60361}
#'
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 3005 cells and 9 clusters in this dataset.
"linnarsson"

#' Single cell RNA-Seq data extracted from a publication by Zhong.
#'
#' Source: Biase, F. H., Cao, X. & Zhong, S. Cell fate inclination within 2-cell
#' and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res.
#' 24, 1787–1796 (2014).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57249}
#'
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 49 cells and 3 clusters in this dataset.
"zhong"

#' Single cell RNA-Seq data extracted from a publication by Kirschner.
#'
#' Source: Klein, A. M. et al. Droplet Barcoding for Single-Cell Transcriptomics
#' Applied to Embryonic Stem Cells. Cell 161, 1187–1201 (2015).
#' 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65525}
#'
#' Columns represent cells, rows represent genes expression values. Colnames
#' respresent indexes of cell clusters (known information based on the 
#' experimental protocol). There are 2717 cells and 3 clusters in this dataset.
"kirschner"