小鼠单细胞注释包-scMCA

scMCA是一种基于单细胞基因表达的鼠细胞类型定义工具。scMCA是简易的R软件包，且有在线版scMCAMouse Cell Atlas 。此外，还添加了一个用于对scMCA进行可视化的UI。

分析流程

1.scMCA R包

安装

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

library(scMCA)
# mca_lung is an example expression matrix from MCA project.
data(mca_lung)
dim(mca_lung)
# scMCA has two parameters , single cell expression matrix(scdata) and 
# the number of most similar cell types
mca_result <- scMCA(scdata = mca_lung, numbers_plot = 3)

The return of scMCA() 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
scMCA: the most relevant cell type for each query cell
scMCA_probility: the top n relevant cell types for each query cell

2. shiny交互式

# open shiny for visualize result for scMCA
scMCA_vis(mca_result)

image.png

3.网页版

原文：scMCA
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