a b/R/data.R
1
#' simulated single cell multi-omics data.
2
#'
3
#' A dataset containing paired single-cell RNA-seq and ATAC-seq data as well as the true labels of cell groups
4
#'
5
#' @format A list contains two field data:
6
#' \describe{
7
#'   \item{data}{Simulated single-cell RNA-seq and ATAC-seq data}
8
#'   \item{labels}{The true labels of cell groups}
9
#'   ...
10
#' }
11
#' @source \url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1932-8}
12
"data_simulation"
13
14
#' A simulation dataset consists of five imbalanced cell clusters with five clusters in scRNA-seq data and three clusters in scATAC-seq data
15
#'
16
#' @format A list contains two field data:
17
#' \describe{
18
#'   \item{data}{Simulated single-cell RNA-seq and ATAC-seq data}
19
#'   \item{labels}{The true labels of cell groups}
20
#'   ...
21
#' }
22
#' @source \url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1932-8}
23
"data_simulation8"
24
25
26
#' single cell multi-omics data of kidney cells.
27
#'
28
#' kidney dataset containing paired single-cell RNA-seq and ATAC-seq data as well as the label information of each cell from the original paper
29
#'
30
#' @format A list contains two field data:
31
#' \describe{
32
#'   \item{data}{Single-cell RNA-seq and ATAC-seq data}
33
#'   \item{labels}{The cell type information of cell groups}
34
#'   ...
35
#' }
36
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089}
37
"data_kidney"
38
39
40
#' single cell multi-omics data of A549 cells.
41
#'
42
#' A549 dataset containing paired single-cell RNA-seq and ATAC-seq data as well as the collected time information of each cell
43
#'
44
#' @format A list contains two field data:
45
#' \describe{
46
#'   \item{data}{Single-cell RNA-seq and ATAC-seq data}
47
#'   \item{labels}{The time information of cell groups}
48
#'   ...
49
#' }
50
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089}
51
"data_A549"
52
53
54
#' single cell multi-omics data of mESC cells.
55
#'
56
#' mESC dataset containing paired single-cell RNA-seq and single-cell methylation data as well as the culture condition information of each cell
57
#'
58
#' @format A list contains two field data:
59
#' \describe{
60
#'   \item{data}{Single-cell RNA-seq and single-cell methylation data}
61
#'   \item{labels}{The culture condition information of cells}
62
#'   ...
63
#' }
64
#' @source \url{https://github.com/bioFAM/MOFA/blob/master/vignettes/MOFA_example_scMT.Rmd}
65
"data_mESC"
66