{"id":13681209,"url":"https://github.com/casecpb/KSEA","last_synced_at":"2025-04-30T03:30:48.476Z","repository":{"id":201292222,"uuid":"81679019","full_name":"casecpb/KSEA","owner":"casecpb","description":"Kinase-Substrate Enrichment Analysis (KSEA) App","archived":false,"fork":false,"pushed_at":"2017-05-02T20:46:23.000Z","size":3657,"stargazers_count":7,"open_issues_count":2,"forks_count":5,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-11-12T00:36:30.136Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/casecpb.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-02-11T20:08:43.000Z","updated_at":"2024-09-05T02:48:56.000Z","dependencies_parsed_at":"2024-06-22T22:03:22.294Z","dependency_job_id":null,"html_url":"https://github.com/casecpb/KSEA","commit_stats":null,"previous_names":["casecpb/ksea"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/casecpb%2FKSEA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/casecpb%2FKSEA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/casecpb%2FKSEA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/casecpb%2FKSEA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/casecpb","download_url":"https://codeload.github.com/casecpb/KSEA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251635036,"owners_count":21619130,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-02T13:01:27.844Z","updated_at":"2025-04-30T03:30:44.745Z","avatar_url":"https://github.com/casecpb.png","language":"R","funding_links":[],"categories":["8. Kinase Motif/Activity Analysis"],"sub_categories":["Table of Contents"],"readme":"# Welcome to the GitHub account for the KSEA App's online tool!\n\n### You can find the source code and all dependent files here!\n\n- **app.R**: the raw R script behind the KSEA App\n- **PSP\u0026NetworKIN_Kinase_Substrate_Dataset_July2016.csv**: the Kinase-Substrate (K-S) dataset that the algorithm uses for identifying the substrates for each kinase\n- **Sample Experimental Dataset.csv**: the sample data file input\n- **User Manual.pdf**: the user manual containing detailed guidelines for navigating through the interface, interpretation of results, troubleshooting, and local installation.\n- **Welcome.Rmd**: the markdown file for the Welcome tab in the KSEA App interface\n- **www**: the folder holding the site's logo and favicon \n\n# Instructions for Local Access via GitHub\n\n### IMPORTANT!\n\nIf you want to analyze your dataset using the KSEAapp R package, go to our sister site https://github.com/casecpb/KSEAapp/ for more details on installation.\n\nIf you want to learn how to run the exact same online interface locally on your computer, continue reading. \n\n**Instructions for local online interface access:**\n1. Download and install the R programming software [here](https://www.r-project.org/). We recommend you have version 3.0.3 or newer installed. This app has not been tested on older versions.\n\n2. Download and install the free R Studio software [here](https://www.rstudio.com/products/rstudio/download/). This provides a useful interface for R programming. \n\n  (This step is optional; if you choose to skip it, steps 3-6 can be done exactly as described within the R program's basic console.)\n\n3. Open R Studio, and install the Shiny package by typing in the following command into your console, and then hit **Enter**. This may take up to a minute for completion. \n  ```\n  install.packages(\"shiny\")\n  ```\n4. Once the “\u003e” symbol and cursor reappear, type in the following code, and then hit **Enter**.\n\n  ```\n  shiny::runGitHub('KSEA', 'casecpb')\n  ```\n5. The KSEA App should then automatically launch in a new window/browser tab. This step may take a few seconds.\n\n6. When finished with the analysis, just exit the interface. Then, if needed, hit the escape (Esc) key within the R studio console to terminate the KSEA App. Ignore the warning messages that may appear, and exit from R Studio. \n\n*Note: steps 1-3 only need to be done once if you are using the same computer. If you wish to access the KSEA App again after the first time, just reopen R Studio, and go straight to step 4.*\n\nInstructions can also be found in the User Manual.\n\n-----\nPlease cite the following papers if using this tool:\n\n1. Wiredja D.D., Koyutürk M., Chance M.R. (2017) The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. *Submitted for review*.\n2. [Casado, P., et al. (2013) Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. *Sci. Signal*. 6, rs6-rs6](http://stke.sciencemag.org/content/6/268/rs6.long)\n3. [Hornbeck P.V., et al. (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. *Nucleic Acids Res*. 43:D512-20](https://academic.oup.com/nar/article/43/D1/D512/2439467/PhosphoSitePlus-2014-mutations-PTMs-and)\n4. [Horn H., et al. (2014) KinomeXplorer: an integrated platform for kinome biology studies. *Nat Methods*. 11(6):603-4](http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2968.html)\n\n-----\nSince the KSEA App is hosted on RStudio's shinyapps.io server and accesses PhosphoSitePlus data, the following must be noted:\n- This tool is intended for non-commercial use.\n- Please read and abide by PhosphoSitePlus's [Terms and Conditions](http://www.phosphosite.org/staticDownloads.action).\n- Please read and abide by RStudio's [Terms of Use](https://www.rstudio.com/about/shinyapps-terms-use/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcasecpb%2FKSEA","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcasecpb%2FKSEA","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcasecpb%2FKSEA/lists"}