ScType 数据库(https://sctype.app)
生信人文章:
https://mp.weixin.qq.com/s/z0pSF8pUC7awegxmKBxwpg
在GitHub上提供了可供使用的R包集代码(https://github.com/IanevskiAleksandr/sc-type/)
开源 R 实现(https://github.com/IanevskiAleksandr/sc-type)
ScType数据库(https://sctype.app/database.php)
总体而言,当前版本的ScType数据库包括17个人体组织中194种细胞类型的3,980个细胞标记物和17个小鼠组织中194种细胞类型的4,212个细胞标记。
先跑下范例数据
##########ScType 示范数据集----
#Quick start
# load libraries and functions
#加载三个包
#install.packages("HGNChelper")
lapply(c("dplyr","Seurat","HGNChelper"), library, character.only = T)
#加载写好的代码
source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/gene_sets_prepare.R");
source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/sctype_score_.R")
# get cell-type-specific gene sets from our in-built database (DB)
#加载参考基因集ScTypeDB_short.xlsx,提取其中的Immune system
gs_list = gene_sets_prepare("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/ScTypeDB_short.xlsx",
"Immune system") # e.g. Immune system, Liver, Pancreas, Kidney, Eye, Brain
#细胞类型中阳性和阴性标记基因
gs_list$gs_positive
gs_list$gs_negative
# assign cell types
#load example scRNA-seq matrix
scRNAseqData = readRDS(gzcon(url('https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/exampleData.RDS')));
#注释
es.max = sctype_score(scRNAseqData = scRNAseqData, scaled = TRUE, gs = gs_list$gs_positive, gs2 = gs_list$gs_negative)
# View results, cell-type by cell matrix. See the complete example below
View(es.max)
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