{"id":25167168,"url":"https://github.com/biocomputingup/cholesterol-model","last_synced_at":"2025-07-12T09:33:50.048Z","repository":{"id":81784667,"uuid":"208271243","full_name":"BioComputingUP/Cholesterol-model","owner":"BioComputingUP","description":null,"archived":false,"fork":false,"pushed_at":"2020-02-12T12:17:41.000Z","size":29,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-04-03T17:53:02.620Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioComputingUP.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-09-13T13:34:04.000Z","updated_at":"2020-02-12T12:17:42.000Z","dependencies_parsed_at":null,"dependency_job_id":"d97f8603-5a7b-49b8-9be9-75ad09391444","html_url":"https://github.com/BioComputingUP/Cholesterol-model","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BioComputingUP/Cholesterol-model","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCholesterol-model","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCholesterol-model/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCholesterol-model/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCholesterol-model/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioComputingUP","download_url":"https://codeload.github.com/BioComputingUP/Cholesterol-model/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioComputingUP%2FCholesterol-model/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264972152,"owners_count":23691375,"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":"2025-02-09T06:19:47.630Z","updated_at":"2025-07-12T09:33:50.040Z","avatar_url":"https://github.com/BioComputingUP.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Scripts ro run in silico model for cholesterol level prediction \n \n\n## REQUIREMENTS\n```\nR:\n\u003einstall.packages('deSolve')\n\u003einstall.packages('pracma')\n\u003einstall.packages('minpack.lm')\n\u003einstall.packages('plotrix')\n\u003einstall.packages('gridExtra)\n\u003einstall.packages('ggplot2')\n```\n\n\n## USAGE\n\nto run all analyses, you have just to run the following command inside the src folder: Rscript ./main_VdP_V01_revision.R\n      This script will compute all statistics and make plots\n      This script expects a folder structure like this to run:\n            * ./src : contains all scripts\n            * ./results : will contain all performance tables and plots\n            * ./results/paper/ : will contain all paper tables and plots    \n            * ./data : will contain all input tables \n      \n      These are Input needed:\n            * input tables in ./data\n\n\n      Running the script these Output files will be generated in ./results\n           * table with fmut optimized (HDL, LDL)\n           * table with fmut optimized (TC), only for DHCR7 gene\n           * boxplot of cholesterol levels (training set)\n           * table with difference between predicted and experimental cholesterol\n           * table with trained vs van de Pas et al. fmut\n           * sensitivity analysis plot (HDL, LDL, TC)\n           * barplot with HDL levels (predicted, real)\n           * table with HDL levels (predicted, real)\n           * barplot with LDL levels (predicted, real)\n           * table with LDL levels (predicted, real)\n           * table with number of mutations and patients for each gene\n           * percentage of difference between predicted and experimental\n           * barplot with TC levels (predicted, real)\n           * table with predicted and real blood cholesterol values\n           * table with PCC, KCC, RMSD and Rsquared of predicted blood cholesterol values\n           * table with TC levels (predicted, real)\n           * table with standard deviation of model predictions\n           * table with bootstrap\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocomputingup%2Fcholesterol-model","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocomputingup%2Fcholesterol-model","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocomputingup%2Fcholesterol-model/lists"}