使用R语言获取人类所有基因的名字，ID，symbol以及别名—科研工具箱

在线查询：https://www.jingege.wang/bioinformatics/gene_alias.html

首先肯定是需要自行搜索了解 entrez gene ID, HUGO symbol, refseq ID, ensembl ID 这些专有名词。

然后直接把下面的代码运行一下，把输出的all_gene_bioconductor.html文件好好看看， 就明白了。

rm(list=ls())
library(org.Hs.eg.db)
eg2symbol=toTable(org.Hs.egSYMBOL)
eg2name=toTable(org.Hs.egGENENAME)
eg2alias=toTable(org.Hs.egALIAS2EG)
eg2alis_list=lapply(split(eg2alias,eg2alias$gene_id),function(x){paste0(x[,2],collapse = \";\")})
GeneList=mappedLkeys(org.Hs.egSYMBOL)
if( GeneList[1] %in% eg2symbol$symbol ){
  symbols=GeneList
  geneIds=eg2symbol[match(symbols,eg2symbol$symbol),\'gene_id\']
}else{
  geneIds=GeneList
  symbols=eg2symbol[match(geneIds,eg2symbol$gene_id),\'symbol\']
}
geneNames=eg2name[match(geneIds,eg2name$gene_id),\'gene_name\']
geneAlias=sapply(geneIds,function(x){ifelse(is.null(eg2alis_list[[x]]),\"no_alias\",eg2alis_list[[x]])})

createLink <- function(base,val) {
   sprintf(\'<a href=\"%s\" class=\"btn btn-link\" target=\"_blank\" >%s</a>\',base,val) 
    ##  target=\"_blank\" 
}
gene_info=data.frame(   symbols=symbols,
                        geneIds=createLink(paste0(\"http://www.ncbi.nlm.nih.gov/gene/\",geneIds),geneIds),
                        geneNames=geneNames,
                        geneAlias=geneAlias,
                        stringsAsFactors = F
) 
#library(\"xtable\") 
#print(xtable(gene_info), type=\"html\",include.rownames=F, file=\'all_gene.anno\',sanitize.text.function = force)
file=\'all_gene_bioconductor.html\'
y <- DT::datatable(gene_info,escape = F,rownames=F)
DT::saveWidget(y,file)

在输出的文件里面可以搜索：