[游戏开发]ecotyper识别细胞类型特异性转录状态

EcoTyper是一个机器学习框架，用于从大量和单细胞（scRNA-seq）表达数据中大规模识别细胞类型特异性转录状态及其联合模式。

1. 下载

git clone https://github.com/digitalcytometry/ecotyper

cd ecotyper

2. 安装依赖包

#运行R，安装依赖包
install.packages(c("NMF", "RColorBrewer", "cluster", "circlize", "cowplot", "data.table", "doParallel", "ggplot2", "grid", "reshape2", "viridis", "config", "argparse", "colorspace", "plyr"))


if (!require("BiocManager", quietly = TRUE))
? ? install.packages("BiocManager")

BiocManager::install("ComplexHeatmap")

3. 简单应用

# 正确的Rscript路径， 当系统有多个R
Rscript EcoTyper_recovery_bulk.R -h

# 1.1. Recovery of Carcinoma Cell States and Ecotypes in Bulk Data
Rscript EcoTyper_recovery_bulk.R -d Carcinoma -m example_data/bulk_lung_data.txt -a example_data/bulk_lung_annotation.txt -c Tissue -o RecoveryOutput

#2.1. Recovery of Carcinoma Cell States and Ecotypes in scRNA-seq Data
Rscript EcoTyper_recovery_scRNA.R -d Carcinoma -m example_data/scRNA_CRC_data.txt -a example_data/scRNA_CRC_annotation.txt -o RecoveryOutput

参考：

https://github.com/digitalcytometry/ecotyper#tutorial-4-de-novo-discovery-of-cell-states-and-ecotypes-in-bulk-data

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