scHCL

A tool defines cell types in human based on single-cell digital expression

At first scHCL is a breif R package for large scale data(large DGE) from scHCL online function Human Cell Landscape ,to alleviate burdens of our main Server.

Now we add a UI for visulizing the scHCL reuslt.

Installation

#This require devtools  
install.packages('devtools')
library(devtools)
# scHCL requires ggplot2/reshape2/plotly/shiny/shinythemes/shiny
install_github("ggjlab/scHCL")

Quick Start

library(scHCL)
# hcl_lung is an example expression matrix from HCL project.
> data(hcl_lung)
> dim(hcl_lung)
[1] 2884   80
# 2884 genes expression value of 80 cells

# scHCL has two parameters , single cell expression matrix(scdata) and 
# the number of most similar cell types
> hcl_result <- scHCL(scdata = hcl_lung, numbers_plot = 3)

The return of scHCL() is a list which contains 4 parts.

• cors_matrix: Pearson correlation coefficient matrix of each cell and cell type.
• top_cors: equals to numbers_plot
• scHCL: the most relevant cell type for each query cell
• scHCL_probility: the top n relevant cell types for each query cell

# open shiny for visualize result for scHCL
scHCL_vis(hcl_result)

scHCL_vis() provides a bref function for visualizing and downloading of scHCL results