代码编织梦想

GPL对应的Bioconductor注释包(最全)

这个是我自己通过代码查找到的GPL对应的bioconductor的注释包,如果是能够找到的话,那么就是这个GPL平台号有应的注释包,如果在这里没有找到的话,那就应该是没有的咯。

一个比较简单实用的方法,在这个网页下,直接快捷键 Ctrl + F, 然后输入你的平台号,就可以快速找到你要的注释包名称了。

至于我如何得到的这个列表,看最底下的代码。

没找到注释包的话,其实你也不要担心,你可以用getGEO 来下载注释信息,进而也能够转换ID。(详细的,以后再看看写不写呗)

gpl96 <- getGEO(‘GPL96’, destdir=“.”) ##根据GPL号下载的是芯片设计的信息!

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在这里插入图片描述

gplbioc_packagetitle
GPL32mgu74a[MG_U74A] Affymetrix Murine Genome U74A Array
GPL33mgu74b[MG_U74B] Affymetrix Murine Genome U74B Array
GPL34mgu74c[MG_U74C] Affymetrix Murine Genome U74C Array
GPL71ag[AG] Affymetrix Arabidopsis Genome Array
GPL72drosgenome1[DrosGenome1] Affymetrix Drosophila Genome Array
GPL74hcg110[HC_G110] Affymetrix Human Cancer Array
GPL75mu11ksuba[Mu11KsubA] Affymetrix Murine 11K SubA Array
GPL76mu11ksubb[Mu11KsubB] Affymetrix Murine 11K SubB Array
GPL77mu19ksuba[Mu19KsubA] Affymetrix Murine 19K SubA Array
GPL78mu19ksubb[Mu19KsubB] Affymetrix Murine 19K SubB Array
GPL79mu19ksubc[Mu19KsubC] Affymetrix Murine 19K SubC Array
GPL80hu6800[Hu6800] Affymetrix Human Full Length HuGeneFL Array
GPL81mgu74av2[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GPL82mgu74bv2[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array
GPL83mgu74cv2[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array
GPL85rgu34a[RG_U34A] Affymetrix Rat Genome U34 Array
GPL86rgu34b[RG_U34B] Affymetrix Rat Genome U34 Array
GPL87rgu34c[RG_U34C] Affymetrix Rat Genome U34 Array
GPL88rnu34[RN_U34] Affymetrix Rat Neurobiology U34 Array
GPL89rtu34[RT_U34] Affymetrix Rat Toxicology U34 Array
GPL90ygs98[YG_S98] Affymetrix Yeast Genome S98 Array
GPL91hgu95av2[HG_U95A] Affymetrix Human Genome U95A Array
GPL92hgu95b[HG_U95B] Affymetrix Human Genome U95B Array
GPL93hgu95c[HG_U95C] Affymetrix Human Genome U95C Array
GPL94hgu95d[HG_U95D] Affymetrix Human Genome U95D Array
GPL95hgu95e[HG_U95E] Affymetrix Human Genome U95E Array
GPL96hgu133a[HG-U133A] Affymetrix Human Genome U133A Array
GPL97hgu133b[HG-U133B] Affymetrix Human Genome U133B Array
GPL98hu35ksuba[Hu35KsubA] Affymetrix Human 35K SubA Array
GPL99hu35ksubb[Hu35KsubB] Affymetrix Human 35K SubB Array
GPL100hu35ksubc[Hu35KsubC] Affymetrix Human 35K SubC Array
GPL101hu35ksubd[Hu35KsubD] Affymetrix Human 35K SubD Array
GPL198ath1121501[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
GPL199ecoli2[Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
GPL200celegans[Celegans] Affymetrix C. elegans Genome Array
GPL201hgfocus[HG-Focus] Affymetrix Human HG-Focus Target Array
GPL339moe430a[MOE430A] Affymetrix Mouse Expression 430A Array
GPL340mouse4302[MOE430B] Affymetrix Mouse Expression 430B Array
GPL341rae230a[RAE230A] Affymetrix Rat Expression 230A Array
GPL342rae230b[RAE230B] Affymetrix Rat Expression 230B Array
GPL570hgu133plus2[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL571hgu133a2[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
GPL886hgug4111aAgilent-011871 Human 1B Microarray G4111A (Feature Number version)
GPL887hgug4110bAgilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
GPL1261mouse430a2[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL1318xenopuslaevis[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array
GPL1319zebrafish[Zebrafish] Affymetrix Zebrafish Genome Array
GPL1322drosophila2[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
GPL1352u133x3p[U133_X3P] Affymetrix Human X3P Array
GPL1355rat2302[Rat230_2] Affymetrix Rat Genome 230 2.0 Array
GPL1708hgug4112aAgilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)
GPL2112bovine[Bovine] Affymetrix Bovine Genome Array
GPL2529yeast2[Yeast_2] Affymetrix Yeast Genome 2.0 Array
GPL2891h20kcodGE Healthcare/Amersham Biosciences CodeLink™ UniSet Human 20K I Bioarray
GPL2898adme16codGE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray
GPL3154ecoli2[E_coli_2] Affymetrix E. coli Genome 2.0 Array
GPL3213chicken[Chicken] Affymetrix Chicken Genome Array
GPL3533porcine[Porcine] Affymetrix Porcine Genome Array
GPL3738canine2[Canine_2] Affymetrix Canine Genome 2.0 Array
GPL3921hthgu133a[HT_HG-U133A] Affymetrix HT Human Genome U133A Array
GPL3979canine[Canine] Affymetrix Canine Genome 1.0 Array
GPL4032[Maize] Affymetrix Maize Genome Array
GPL4191h10kcodCodeLink UniSet Human I Bioarray
GPL5188huex10sttranscriptcluster[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
GPL5689hgug4100aAgilent Human 1 cDNA Microarray (G4100A) [layout C]
GPL6097illuminaHumanv1Illumina human-6 v1.0 expression beadchip
GPL6102illuminaHumanv2Illumina human-6 v2.0 expression beadchip
GPL6244hugene10sttranscriptcluster[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
GPL6246mogene10sttranscriptcluster[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GPL6885illuminaMousev2Illumina MouseRef-8 v2.0 expression beadchip
GPL6947illuminaHumanv3Illumina HumanHT-12 V3.0 expression beadchip
GPL8300hgu95av2[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array
GPL8321mouse430a2[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array
GPL8490IlluminaHumanMethylation27kIllumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
GPL10558illuminaHumanv4Illumina HumanHT-12 V4.0 expression beadchip
GPL11532hugene11sttranscriptcluster[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]
GPL13497HsAgilentDesign026652Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)
GPL13534IlluminaHumanMethylation450kIllumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL13667hgu219[HG-U219] Affymetrix Human Genome U219 Array
GPL14877hgu133plus2Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG]
GPL15380GGHumanMethCancerPanelv1Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I
GPL15396hthgu133b[HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]
GPL17556hugene10sttranscriptcluster[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0]
GPL17897hthgu133a[HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)
GPL18190hugene11sttranscriptcluster[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]

这个代码的来源地址是在:
https://grokbase.com/t/r/bioconductor/10346g1y52/bioc-annotation-for-a-geo-data-set

只不过这里的情况是,getSQLiteFile()这一步下载数据很大(大概在540MB),用R下载的时候会比较慢,然后解压出来的文件达到8GB。所以如果你的电脑内存少于8GB,就不建议你去运行这个代码了。

library(GEOmetadb)
sqlfile = getSQLiteFile()
con = dbConnect("SQLite",sqlfile)
Y = dbGetQuery(con,"select gpl,title,bioc_package from gpl where gpl='GPL570'"") #找到GPL570对应的R包。
#Then, you are off to the races....
biocLite('hgu133plus2.db')

我的代码如下,但是前提是你得先去用下载这个sql文件,该文件的下载地址(可以这里直接点击下载)是
http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz

下载完成后要解压这个文件,最后的文件名应该是GEOmetadb.sqlite, 可能以后这个会改,注意一下代码里面的文件名和路径就是了。

library(GEOmetadb)
con <- dbConnect(SQLite(), "GEOmetadb.sqlite/GEOmetadb.sqlite")
dat <- dbGetQuery(con, "select * from metaInfo")
#dbDisconnect(con)

Y = dbGetQuery(con,"select gpl,title,bioc_package from gpl")
Y = na.omit(Y)

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