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perslab / depict

DEPICT code, instructions and an example
GNU General Public License v3.0
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Some data resource are missing #8

Open Bochao1 opened 7 years ago

Bochao1 commented 7 years ago

Dear all,

I am new user for DEPICT. I went through the DEPICT example script. It works well in my PC. However, I found some data is missing from the downloaded newest version package. If they are missing, how did I run the example script well and get the expected output (are these data used outside of DEPICT/data by default)? Is any way I can access and download these data? The missing data items remain below:

Precomputed loci for each 1000 Genomes project SNPs

collection_file: data/collections/ld0.5_collection_1000genomespilot_depict_150429.txt.gz

The tissue expression matrix

tissue_expression_file: data/tissue_expression/GPL570EnsemblGeneExpressionPerTissue_DEPICT20130820_z_withmeshheader.txt

Mapping from tissue/cell type identifier to tissue name and information

tissue_mapping_file: data/tissue_expression/GPL570EnsemblGeneExpressionPerTissue_DEPICT20130820_z_withmeshheader_mapping.txt

Gene annotation file

depict_gene_annotation_file: data/mapping_and_annotation_files/GPL570ProbeENSGInfo+HGNC_reformatted.txt

Bochao1 commented 7 years ago

I think I found them, which is available to download from website: https://data.broadinstitute.org/mpg/depict/documentation.html