小鼠单细胞注释包-scMCA---生信编程日常

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)

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