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有很多已经按照芯片平台处理好的表达量数据可以直接分析

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发表于 2016-11-27 15:54:20 | 显示全部楼层 |阅读模式
http://seek.princeton.edu/download.jsp
还是蛮有用的:Search-Based Exploration of Expression Compendium [Hum
an]
只分析表达数据,都是人工curated的芯片平台
21700 genes in human
4929 mRNA microarray datasets
281 RNASeq datasets
48 platforms


    Below are the links to download the processed and normalized gene expression datasets that are used in the SEEK human compendium. These datasets are organized by platform.This data collection has been uniformly processed according to platform, and as such, it can be useful for doing coexpression, differential expression, and other downstream analyses both within and across datasets.



  • GPL570.tar.gz 3.6G, 1960 datasets[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
  • GPL96.tar.gz 814M, 516 datasets[HG-U133A] Affymetrix Human Genome U133A Array
  • GPL6244.tar.gz 622M, 394 datasets[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
  • GPL5175.tar.gz 177M, 120 datasets[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
  • GPL571.tar.gz 276M, 269 datasets[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
  • GPL8300.tar.gz 66M, 96 datasets[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array
  • GPL1708.tar.gz 80M, 69 datasetsAgilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)
  • GPL4133.tar.gz 397M, 331 datasetsAgilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
  • GPL6480.tar.gz 352M, 310 datasetsAgilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
  • GPL6884.tar.gz 243M, 107 datasetsIllumina HumanWG-6 v3.0 expression beadchip
  • GPL6947.tar.gz 383M, 180 datasetsIllumina HumanHT-12 V3.0 expression beadchip
  • TCGA.RNASeq.tar.gz 279M, 224 datasetsTCGA RNASeq V2 collection




    How to view the *.bin files in the tar ball?
    Each .bin file is an expression matrix in the binary format. To view its content, convert it to the text format using the PCL2Bin tool available in the Sleipnir toolkit. (You would need to first install Sleipnir if you do not already have it in your system. PCL2Bin is one of the tools in the toolkit. Alternatively, you can use a pre-compiled executable of PCL2Bin available here.)Next enter the following:
    PCL2Bin -i GSE10107.GPL4133.pcl.bin -o GSE10107.GPL4133.pcl
    This is an example script. -i is the input file. -o is the output text file. In the output file, the columns are samples; the rows are genes in ENTREZ gene IDs; the values are log-normalized.






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发表于 2017-7-14 13:49:38 | 显示全部楼层
你好,请问你有下到编译好的PCL2Bin么?下面说明里面貌似没有加链接,我找了半天也不知道他们把下载放在哪里
How to view the *.bin files in the tar ball?

Each .bin file is an expression matrix in the binary format. To view its content, convert it to the text format using the PCL2Bin tool available in the Sleipnir toolkit. (You would need to first install Sleipnir if you do not already have it in your system. PCL2Bin is one of the tools in the toolkit. Alternatively, you can use a pre-compiled executable of PCL2Bin available here.)

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发表于 2018-1-17 13:30:03 | 显示全部楼层
好东西,感谢分享
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