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Update README.md
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yil8 committed Dec 21, 2017
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The original data files are not provided within this codebase, as some of them require applying for access. Once you download all of them, please put them in this codebase.

GEO
GEO and GTEx
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The GEO microarray expression data can be accessed from [lincscloud](http://www.lincscloud.org/l1000/). You need to [apply](https://docs.google.com/forms/d/1j6Vb_s4FrDodxoS3IDZsHWoVNrOnKNQbqwbwcW2a208/viewform) for the access. The original data downloaded is **bgedv2_QNORM.gctx** (data level 3 Q2NORM).

**UPDATE1**: It seems lincscloud has been migrated to NCH: http://www.lincscloud.org/download.html . And the data is publicly available now at [GSE70138](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138):**GSE70138_Broad_LINCS_Level3_INF_mlr12k_n115209x22268_2015-12-31.gct.gz**. However, the number of samples is slightly different (129158 vs 115209). Not sure if the current code base works fine for this new data. Will take a look in the furture.

**UPDATE2**: Since the data provided in **UPDATE1** is slightly different than the original GEO version we used in our publiction, please email us (yil8@uci.edu) if you could like to download the original version.


GTEx
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The GTEx data we used in our paper is a preliminary version from the Broad institute before the official publication of GTEx, and is not publicly available. For those who are interested in the data, please email us (yil8@uci.edu) with your basic information through an academic institute email address, and we will provide you the private download link. The data you will download is **GTEx_RNASeq_RPKM_n2921x55993.gctx**.

The GEO and GTEx data we used in our paper is a preliminary version before their official publication, and is not publicly available. For those who are interested in the data, please email us (yil8@uci.edu) with your basic information through an academic institute email address, and we will provide you the private download link. The data you will download is **bgedv2_QNORM.gctx** and **GTEx_RNASeq_RPKM_n2921x55993.gctx**.

1000G
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