library(org.Hs.eg.db )
This online tool currently uses CrossMap, which supports a limited number of formats (see our online documentation for details of the individual data formats listed below). CrossMap also discards metadata in files, so track definitions, etc, will be lost on conversion.
Important note: CrossMap converts WIG files to BedGraph internally for efficiency, and also outputs them in BedGraph format.
因为大部分生物信息学软件都是linux版本的，所以生物信息学数据分析工作者必备技能就是linux，但是大部分人只是拿他当个中转站，我以前也是，直到接触了大批量的任务，自动化流程，才明白这里面的水太深了，不过无所谓，凭我个人的观点，其实shell的进阶语法真的不必要！
我也不想去搞明白操作符两边是否加空格的区别是什么了。
如果，还有其它功能需要实现，我们可以把脚本写的更负载，纯粹的用shell，需要搜索更多的shell技巧。
[perl]
## perl nohup.pl deep_count.sh 0
## perl nohup.pl deep_count.sh 1
## perl nohup.pl deep_count.sh 2
$i=1;
open FH,$ARGV[0];
while(<FH>){
chomp;
next unless $.%3==$ARGV[1];
$cmd="nohup $_ &";
print "$cmd\n";
system($cmd);
sleep(10800) if $i%5==4;
$i++;
#exit;
}
[/perl]
[perl]
suppressMessages(library(ggplot2))
suppressMessages(library(RMySQL))
con <- dbConnect(MySQL(), host="127.0.0.1", port=3306, user="root", password="11111111")
dbSendQuery(con, "USE test")
gene='SOX10'
#gene='DDX11L11'
if (T){
query=paste("select * from hg19_gtf where gene_type='protein_coding' and gene_name=",shQuote(gene),sep="")
structure=dbGetQuery(con,query)
tmp_min=min(c(structure$start,structure$end))
structure$new_start=structure$start-tmp_min
structure$new_end=structure$end-tmp_min
tmp_max=max(c(structure$new_start,structure$new_end))
num_transcripts=nrow(structure[structure$record=='transcript',])
tmp_color=rainbow(num_transcripts)
x=1:tmp_max;y=rep(num_transcripts,length(x))
#x=10000:17000;y=rep(num_transcripts,length(x))
plot(x,y,type = 'n',xlab='',ylab = '',ylim = c(0,num_transcripts+1))
title(main = gene,sub = paste("chr",tmp$chr,":",tmp$start,"-",tmp$end,sep=""))
j=0;
tmp_legend=c()
for (i in 1:nrow(structure)){
tmp=structure[i,]
if(tmp$record == 'transcript'){
j=j+1
tmp_legend=c(tmp_legend,paste("chr",tmp$chr,":",tmp$start,"-",tmp$end,sep=""))
}
if(tmp$record == 'exon') lines(c(tmp$new_start,tmp$new_end),c(j,j),col=tmp_color[j],lwd=4)
}
# legend('topleft',legend=tmp_legend,lty=1,lwd = 4,col = tmp_color);
}
[/perl]
刚开始接触生物信息学的时候我也很纠结什么fastq,fastq,sam,bam,vcf,maf,gtf,bed,psl等等，甚至还有过时了的NCBI,ENSEMBL格式，如果是我刚开始 学的时候，我倒是很愿意把他们全部搞透彻，写详细的说明书，但是现在成长了，这些东西感觉很low了，正好我看到了一篇帖子讲数据格式的收集大全，分享给大家，希望初学者能多花点时间好好钻研！
https://www.biostars.org/p/55351/
现有的基因芯片种类不要太多了！
gpl organism bioc_package1 GPL32 Mus musculus mgu74a2 GPL33 Mus musculus mgu74b3 GPL34 Mus musculus mgu74c6 GPL74 Homo sapiens hcg1107 GPL75 Mus musculus mu11ksuba8 GPL76 Mus musculus mu11ksubb9 GPL77 Mus musculus mu19ksuba10 GPL78 Mus musculus mu19ksubb11 GPL79 Mus musculus mu19ksubc12 GPL80 Homo sapiens hu680013 GPL81 Mus musculus mgu74av214 GPL82 Mus musculus mgu74bv215 GPL83 Mus musculus mgu74cv216 GPL85 Rattus norvegicus rgu34a17 GPL86 Rattus norvegicus rgu34b18 GPL87 Rattus norvegicus rgu34c19 GPL88 Rattus norvegicus rnu3420 GPL89 Rattus norvegicus rtu3422 GPL91 Homo sapiens hgu95av223 GPL92 Homo sapiens hgu95b24 GPL93 Homo sapiens hgu95c25 GPL94 Homo sapiens hgu95d26 GPL95 Homo sapiens hgu95e27 GPL96 Homo sapiens hgu133a28 GPL97 Homo sapiens hgu133b29 GPL98 Homo sapiens hu35ksuba30 GPL99 Homo sapiens hu35ksubb31 GPL100 Homo sapiens hu35ksubc32 GPL101 Homo sapiens hu35ksubd36 GPL201 Homo sapiens hgfocus37 GPL339 Mus musculus moe430a38 GPL340 Mus musculus mouse430239 GPL341 Rattus norvegicus rae230a40 GPL342 Rattus norvegicus rae230b41 GPL570 Homo sapiens hgu133plus242 GPL571 Homo sapiens hgu133a243 GPL886 Homo sapiens hgug4111a44 GPL887 Homo sapiens hgug4110b45 GPL1261 Mus musculus mouse430a249 GPL1352 Homo sapiens u133x3p50 GPL1355 Rattus norvegicus rat230251 GPL1708 Homo sapiens hgug4112a54 GPL2891 Homo sapiens h20kcod55 GPL2898 Rattus norvegicus adme16cod60 GPL3921 Homo sapiens hthgu133a63 GPL4191 Homo sapiens h10kcod64 GPL5689 Homo sapiens hgug4100a65 GPL6097 Homo sapiens illuminaHumanv166 GPL6102 Homo sapiens illuminaHumanv267 GPL6244 Homo sapiens hugene10sttranscriptcluster68 GPL6947 Homo sapiens illuminaHumanv369 GPL8300 Homo sapiens hgu95av270 GPL8490 Homo sapiens IlluminaHumanMethylation27k71 GPL10558 Homo sapiens illuminaHumanv472 GPL11532 Homo sapiens hugene11sttranscriptcluster73 GPL13497 Homo sapiens HsAgilentDesign02665274 GPL13534 Homo sapiens IlluminaHumanMethylation450k75 GPL13667 Homo sapiens hgu21976 GPL15380 Homo sapiens GGHumanMethCancerPanelv177 GPL15396 Homo sapiens hthgu133b78 GPL17897 Homo sapiens hthgu133a
gpl_info=read.csv("GPL_info.csv",stringsAsFactors = F)### first download all of the annotation packages from bioconductorfor (i in 1:nrow(gpl_info)){print(i)platform=gpl_info[i,4]platform=gsub('^ ',"",platform) ##主要是因为我处理包的字符串前面有空格#platformDB='hgu95av2.db'platformDB=paste(platform,".db",sep="")if( platformDB %in% rownames(installed.packages()) == FALSE) {BiocInstaller::biocLite(platformDB)#source("http://bioconductor.org/biocLite.R");#biocLite(platformDB )}}
下载完了所有的包， 就可以进行批量导出芯片探针与gene的对应关系！
for (i in 1:nrow(gpl_info)){print(i)platform=gpl_info[i,4]platform=gsub('^ ',"",platform)#platformDB='hgu95av2.db'platformDB=paste(platform,".db",sep="")if( platformDB %in% rownames(installed.packages()) != FALSE) {library(platformDB,character.only = T)#tmp=paste('head(mappedkeys(',platform,'ENTREZID))',sep='')#eval(parse(text = tmp))###重点在这里，把字符串当做命令运行all_probe=eval(parse(text = paste('mappedkeys(',platform,'ENTREZID)',sep='')))EGID <- as.numeric(lookUp(all_probe, platformDB, "ENTREZID"))##自己把内容写出来即可}}
| Hugo_Symbol | HUGO symbol for the gene | TP53 |
| Protein_Change | Amino acid change | V600E |
Pfam provides an online tool to not only generate the domain information in JSON format, but to draw the lollipop diagram using javascript as well. They have more information here: http://pfam.xfam.org/help#tabview=tab9
IMHO, not as pretty as cBioPortal's but it gets you close to a solution.
EDIT / SHAMELESS PLUG: After seeing the data available and how easy it'd be, I made my own quick tool to fetch the data and draw the diagram for me in a style similar to cBioPortal - feel free to fork it and add features: https://github.com/pbnjay/lollipops
Example output (w/ labels per the comments)
We found ourselves in the same need, we wanted such a plot (JavaScript). Thus, I add our solution, Mutations Needle Plot. The library creates an SVG image (with D3), which then may be downloaded.
You will npm in order to be able to install & run the library.
Examples may be found in the snippets folder or also the index.html - The one displayed here below
很多时候，我们都无法确定到底是基于symbol来进行分析，还是基于entrez ID，当我们要进行ID转换的时候也想当然的以为它们的一一对应的， 但是最近我写了一个脚本来分析CCLE的数据的时候，发现其实有一些特例:
all_symbol=mappedkeys(org.Hs.egSYMBOL2EG)
我现在还不是很确定这个方法，只是试一试，欢迎与我交流对该方法的讨论！
Wang H, Sun Q, Zhao W, et al. Individual-level analysis of differential expression of genes and pathways for personalized medicine[J]. Bioinformatics, 2014: btu522.
他们把它写成了一个R包，可以下载使用，但是必须用R2.15.2版本，我用了一下，不好用！
We can download the R code for in http://bioinformatics.oxfordjournals.org/content/31/1/62/suppl/DC1
他们这个程序真心不好用，但是很容易看懂算法，可以自己用R语言写一个来实现同样的过程！
用my.surv <- surv(OS_MONTHS,OS_STATUS=='DECEASED')构建生存曲线。用kmfit2 <- survfit(my.surv~TUMOR_STAGE_2009)来做某一个因子的KM生存曲线。用 survdiff(my.surv~type, data=dat)来看看这个因子的不同水平是否有显著差异，其中默认用是的logrank test 方法。用coxph(Surv(time, status) ~ ph.ecog + tt(age), data=lung) 来检测自己感兴趣的因子是否受其它因子(age,gender等等)的影响。
如果只是画网络图，那么只需要把所有的点，按照算好的坐标画出来，然后把所有的连线也画出即可！
接下来， 我们直接看看R里面是如何画网络图的，我们首推一个包：networkD3/
报错如下：ERROR MESSAGE: SAM/BAM file input.marked.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups ！
A general framework for estimating the relative pathogenicity of human genetic variants.
Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.
PubMed PMID: 24487276.
Your search returned 207 results in 9 categories with the following search parameters:
| BIND | the biomolecular interaction network database | died link |
| DIP | the database of interacting proteins | http://dip.doe-mbi.ucla.edu/ |
| MINT | the molecular interaction database | http://mint.bio.uniroma2.it/mint/ |
| STRING | Search Tool for the Retrieval of Interacting Genes/Proteins | http://string-db.org/ |
| HPRO | Human protein reference database | http://www.hprd.org/ |
| BioGRID | The Biological General Repository for Interaction Datasets | http://thebiogrid.org/ |
