Day1-jam

效率工具

chrome(一直就是使用谷歌，推荐风车云马这一款梯子，主要是稳定）

Everthing

snipaste

桌面版微信

笔记整理

幕布（学生可以免费领取一年会员）

image.png

Xmind（使用过，不及幕布）

学习一段代码如下（使用compareCluster函数）对应帖子

if(!require("clusterProfiler")) BiocManager::install("clusterProfiler",ask = F,update = F)
library(clusterProfiler)
if(!require("org.Mm.eg.db")) BiocManager::install("org.Mm.eg.db",ask = F,update = F)
library(org.Mm.eg.db)
tmp <- bitr(group_g$gene,fromType = "ENSEMBL",
            toType = "ENTREZID",
            OrgDb = "org.Mm.eg.db")
de_gene_cluster <- merge(tmp,group_g,by.x="ENSEMBL",by.y="gene")
table(de_gene_cluster$group)

###run go analysis
formula_res <- compareCluster(
  ENTREZID~group,
  data = de_gene_cluster,
  fun = "enrichGO",
  OrgDb = "org.Mm.eg.db",
  style="margin: 0px; padding: 0px; font-size: inherit; line-height: inherit; color: rgb(80, 161, 79); overflow-wrap: inherit !important; word-break: inherit !important;">"BP",
  pAdjustMethod = "BH",
  pvalueCutoff = 0.01,
  qvalueCutoff = 0.05
)

lineage1_ego <-simplify(
  formula_res,
  cutoff=0.5,
  by="p.adjust",
  select_fun=min
)
save(group_g,formula_res,lineage1_ego,file="step5_GOananlysis.Rdata")
#出图
pdf("figures/step5_Microglia_GO_term_DE.pdf",width = 15,height = 15)
dotplot(lineage1_ego,showCategory=10)
dev.off()
write.csv(lineage1_ego@compareClusterResult,
          file="figures/Microglia_GO_term_DE.csv")

markdown学习链接