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HCA-reproducibility

A case study on the detailed reproducibility of a human cell atlas project

Data description

  • Data.RData: data from the original paper, including:

    • discovery.dataset : discovery dataset with 1140 cells
    • validation.dataset : validation dataset with 1244 cells
    • all.label : refined cell type for 1077 out of the 1140 cells in the discovery datasets
    • given.markers : Maker genes for DC1--DC6

  • Reproduced.dc.markers.RData : marker genes identified using data for DCs.

  • Reproduced.mono.dc.markers.RData : marker genes identified using data for both DCs and monocytes.

R packages

The most of reprodcution work were done using the Package Seurat (2.3.4). There are also some other helpful packages. Run the following code to install all these packages.

install.packages(c("Seurat","plyr", 'dplyr', "reshape2", "ggpubr", "VennDiagram"))

Reference

  • A. C. Villani et al., "Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors," Science, vol. 356, no. 6335, Apr 21 2017.
  • A. Butler, P. Hoffman, P. Smibert, E. Papalexi, and R. Satija, "Integrating single-cell transcriptomic data across different conditions, technologies, and species," Nat Biotechnol, vol. 36, no. 5, pp. 411-420, Jun 2018.