单细胞数据集

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60361

library(tidyverse)
library(Seurat)
library(Matrix)

exprMatrix <- read_delim("testData/singlecell/GSE60361_C1-3005-Expression.txt.gz")  |>
  distinct(cell_id, .keep_all = TRUE) |>
  column_to_rownames("cell_id")
exprMatrix[1:5,1:5]
# rownames(My_data) <- My_data[,1]
# My_data <- My_data[,-1]

Matx <- as.matrix(exprMatrix)
Matx <- as(Matx,"sparseMatrix")
seurat_ob <- CreateSeuratObject(counts = Matx)
seurat_ob@assays$RNA@counts[1:5,1:5]

monocle lung 数据

原始位置: monocle-release/R/utils.R，monocle-release/inst/extdata/
测试数据: https://gitee.com/bioinfoFungi/monocle2/tree/master/monocle2_lung

表达矩阵

lung_exprs_data <- readr::read_tsv("https://gitee.com/bioinfoFungi/monocle2/raw/master/monocle2_lung/lung_exprs_data.tsv",show_col_types = FALSE) |>
    column_to_rownames("symbol")
lung_exprs_data[1:5,1:5]

样本信息

lung_phenotype_data <- readr::read_tsv("https://gitee.com/bioinfoFungi/monocle2/raw/master/monocle2_lung/lung_phenotype_data.tsv",show_col_types = FALSE) |>
    column_to_rownames("sample")
lung_phenotype_data[1:5,1:5] 

基因信息

lung_feature_data <- readr::read_tsv("https://gitee.com/bioinfoFungi/monocle2/raw/master/monocle2_lung/lung_feature_data.tsv",show_col_types = FALSE) |>
    column_to_rownames("symbol")
lung_feature_data[1:5,1:5]

monocle HSMM（human skeletal muscle myoblasts） 数据

原始位置：monocle-release/tests/testthat/test.plot_cell_clusters.R，Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)

library(HSMMSingleCell)
data(HSMM_expr_matrix)
data(HSMM_gene_annotation)
data(HSMM_sample_sheet)