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Murphy Lab - Software - PLoS ONE 2012 - Classification and ReannotationThe software and intermediate results used for the following paper can be downloaded below: Jieyue Li, Justin Y. Newberg, Mathias Uhlen, Emma Lundberg, and Robert F. Murphy. Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas. (2012) PLoS ONE 7:e0050514. The data and code are contained in the following files compressed with tar with the -z option (gzip) Recreating Final Results from Raw Image DataTo recreate the results from the article (i.e. the figures and tables) from the raw image data,Download and expand the source code to the desired directory. tar -xzf HPA_reannotation_onlycode.tgz Download and expand one or more of the tgz files of raw images, e.g.: tar -xzf HPA_reannotation_rawdataHPA_A431-1.tgz You can also use the helper script getrawdata.sh to download and extract all of the raw images (approximately 70GB). In Matlab, run the main script >> masterscript See details in masterscript.m for more options of input image path. Recreating Final Results from Intermediate ResultsRecreate the results from the article (i.e. the figures and tables), from intermediate results of classification and reannotationTo recreate the final results from the intermediate results of classification and reannotation, download the source code and intermediate results to the desired directory and expand them.tar -xzf HPA_reannotation_onlycode.tgz tar -xzf HPA_reannotation_intermediate.tgz In Matlab, run the function >> regenResults System requirements
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Last Updated: 02 Dec 2012 |
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