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\n\n\n## GRcalculator dockerfile\n\nThe dockerfile in this container builds a docker image (https://hub.docker.com/r/ucbd2k/grcalculator-docker/) that contains an RStudio/Shiny Server installation with minimum R package and external dependencies for running the GRcalculator applications. The dockerfile clones git repositories for the three R/Shiny apps deployed at http://www.grcalculator.org and installs them inside the docker image. See below for more details on the applications and links to their code repositories.\n\n## GRcalculator: an online tool for calculating and mining drug response data\n\nGRcalculator is a Shiny application (http://www.grcalculator.org) developed to accompany the Nature paper *Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs* by Hafner et al. (2016).\n\nFor a brief overview of the GRcalculator and the importance of the newly developed GR metrics methodology (Hafner et al. 2016), see this poster:\nhttps://figshare.com/articles/GRcalculator_an_online_tool_for_calculating_and_mining_drug_response_data/4244408\n\n#### Citations\n\nClark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, et al. GRcalculator: an online tool for calculating and mining dose–response data. BMC Cancer 2017, 17(1):698. (https://doi.org/10.1186/s12885-017-3689-3)\n\nHafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nature Methods 2016, 13(6):521-527. (https://doi.org/10.1038/nmeth.3853)\n\n#### Website design and online tool development\n\nNick Clark¹, Marc Hafner², Michal Kouril¹, Mario Niepel², Elizabeth Williams², Jeremy Muhlich² and Mario Medvedovic¹\n\n¹ LINCS-BD2K Data Coordination and Integration Center, **University of Cincinnati**\n\n² HMS LINCS Center, **Harvard Medical School**\n\n## Offline installation\n\nInstall R package dependencies:\n\n```r\n# Install our \"GRmetrics\" Bioconductor package and others\nsource(\"http://bioconductor.org/biocLite.R\")\nbiocLite(\"GRmetrics\")\nbiocLite(\"S4Vectors\")\n# Install our \"shinyLi\" package\ninstall.packages(\"devtools\")\ndevtools::install_github(\"uc-bd2k/shinyLi\")\n# Install CRAN package dependencies\ninstall.packages(c(\"shiny\",\"shinyjs\",\"shinyBS\",\"ggplot2\",\"plotly\",\"drc\",\"stringr\",\"readr\"))\n\n```\nRun the application from the R command line:\n```r\nshiny::runGitHub('uc-bd2k/grcalculator')\n```\n## Related software\nThe GRcalculator tool (http://www.grcalculator.org) is implemented in the form of three integrated Shiny applications (grcalculator, grbrowser and grtutorial).\n\n### grtutorial (https://github.com/uc-bd2k/grtutorial)\nThe grtutorial Shiny application (“About GR Metrics” link in the toolbar) provides background information about the advantages of the GR metrics over traditional metrics for quantifying dose-response assays as well as descriptions of the GRcalculator tools.\n\n### grbrowser (https://github.com/uc-bd2k/grbrowser)\nThe grbrowser Shiny application (“LINCS Dose-Response Datasets” section in the toolbar) facilitates interactive browsing and mining of drug response data generated by the LINCS project.\n\n### GRmetrics R package (https://github.com/uc-bd2k/GRmetrics)\nThis package re-creates the online calculation and visualization tools available at http://www.grcalculator.org/grcalculator/.\n\n**Bioconductor page**: https://bioconductor.org/packages/GRmetrics\n\n**Vignette**: https://bioconductor.org/packages/release/bioc/vignettes/GRmetrics/inst/doc/GRmetrics-vignette.html\n\n```R\n# Use the following code to install the GRmetrics package in R\nsource(\"http://bioconductor.org/biocLite.R\")\nbiocLite(\"GRmetrics\")\n```\n\n### MATLAB and Python tools (https://github.com/datarail/gr_metrics)\nThis repository contains the MATLAB, Python, and R implementations of GR metrics calculations with examples and supplementary information.\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",961312421,"orgData","recentTags",[87],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_97":98,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},"content_type","creator",1499341,"digest","sha256:2bc5f81cce51d826a0e24fc90533800e507613dad48d40d47f0374aa1685b837","full_size",961291733,"id",470001838,"images",[99],{"_100":101,"_91":92,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":94,"_59":62,"_112":-5},"architecture","amd64","features","last_pulled","2026-09-26T21:44:45.673722854Z","last_pushed","2023-07-06T00:43:32Z","os","linux","os_features","os_version","size","variant","2023-07-06T00:43:31.188092Z","last_updater","last_updater_username","media_type","base","repository",20426320,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":135,"_142":143,"_131":152,"_153":11},{"_36":136,"_38":137,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":138,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":139,"_75":11,"_76":141,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":140},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_144":60,"_145":-5,"_146":-5,"_147":148},"count","next","previous","results",[149],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_97":150,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},[151],{"_100":101,"_91":92,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":94,"_59":62,"_112":-5},[],"canDeleteTags","actionData","errors"]

applibs/grcalculator-docker-base

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