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R 批量读取文件夹里的文件

R 选色

Degseq 用法

火山图仅需要pval 和log2FoldChangev_circ$color <- ifelse(v_circ$pval <0.05 & abs(v_circ$log2FoldChange)>= 1,ifelse(v_circ$log2FoldChange > 1,'red','blue'),'gray')color <- c(red = "red",gray = "gray",blue = "blue")circ_vo <- ggplot(v_circ

ex <- rownames_to_column(ex)ex$DESCRIPTION <- 'na'ex <- relocate(ex, DESCRIPTION, .after = rowname)write.table(ex, 'ex.txt', sep = '\t',quote = FALSE,row.names = F)GSEA 软件需要输入有一列DESCRIPTION。可以用‘NA’填充。

x_t <- t(x)y_t <- t(y)cor_result <- as.data.frame(cor(x,y))cor_result <- rownames_to_column(cor_result)cor_result <- pivot_longer(cor_result, -rowname)library(ggcorrplot)这个包可以用于可视化相关性矩阵的结果

library(readr)library(topGO)library(KEGGREST)library(clusterProfiler)library(org.Hs.eg.db)library(tidyverse)test1 = bitr(gene, fromType="SYMBOL", toType=c("ENSEMBL", "ENTREZID"), OrgDb="org.Hs.eg.db")ego_ALL <- enrichGO(gene = test1$ENTREZID,

a$type <- 'Up'a$type[a$b < -1] <- 'down'

R seqinr从一个有多个序列的fasta文件中， 批量选择所需要的文件library(seqinr)all_fasta <- read.fasta('fasta.fasta')#这一步把名字换成想要的样子names(all_fasta) <- gsub(":.*", "", names(all_lncfasta))#选取sub_fasta <- all_fasta[names(all_fasta) %in% target_list$name]# 写出文件wri

R gsuba <- gsub("\\..*", "", a)\ escape the special characrer ..* meanseverything after . will be replaced by “”

My gene 转换idconverter <- queryMany(gene_list, scope = "symbol", fields= c('ensembl.gene'), species = 'human')gene_id_after_converter <- unlist(converter$ensembl)unlist 用于解开返回的id name 值

R 安装包失败尝试安装二进制版本。BiocManager::install(“rtracklayer”, type = ‘binary’)