{"id":16849130,"url":"https://github.com/cbrueffer/mutationexplorer","last_synced_at":"2025-04-05T10:42:39.575Z","repository":{"id":54189691,"uuid":"155291747","full_name":"cbrueffer/MutationExplorer","owner":"cbrueffer","description":"R Shiny based lightweight mutation exploration tool","archived":false,"fork":false,"pushed_at":"2021-03-04T09:29:17.000Z","size":362,"stargazers_count":3,"open_issues_count":7,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-10T21:37:16.838Z","etag":null,"topics":["bioinformatics","cancer","cancer-genomics","mutations","r","rna-seq","scanb","shiny","shinyapp","somatic-mutations"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cbrueffer.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}},"created_at":"2018-10-29T22:51:06.000Z","updated_at":"2023-05-25T19:25:04.000Z","dependencies_parsed_at":"2022-08-13T08:50:13.463Z","dependency_job_id":null,"html_url":"https://github.com/cbrueffer/MutationExplorer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbrueffer%2FMutationExplorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbrueffer%2FMutationExplorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbrueffer%2FMutationExplorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbrueffer%2FMutationExplorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbrueffer","download_url":"https://codeload.github.com/cbrueffer/MutationExplorer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247325645,"owners_count":20920713,"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":["bioinformatics","cancer","cancer-genomics","mutations","r","rna-seq","scanb","shiny","shinyapp","somatic-mutations"],"created_at":"2024-10-13T13:14:09.542Z","updated_at":"2025-04-05T10:42:39.556Z","avatar_url":"https://github.com/cbrueffer.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MutationExplorer\n\nMutationExplorer is a lightweight web application for exploring somatic mutations in cancer datasets.  It is based on R and the Shiny framework.\n\nMutationExplorer is currently most usable for breast cancer samples, since the relevant biomarkers for patient selection (e.g. clinical status of ER and PgR) are hardcoded.\n\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"https://github.com/cbrueffer/MutationExplorer/blob/master/doc/images/mutationexplorer-main.png\" width=\"600\" height=\"330\" /\u003e\n\u003c/p\u003e\n\n\n## Features\n\n- Filtering of mutations by type (nonsense, missense, etc) and [COSMIC](https://cancer.sanger.ac.uk/cosmic/) status\n- Filtering of the patient sample cohort by histological/genomic biomarker status\n- Mutational landscape waterfall plots\n- Kaplan-Meier survival analysis based on gene and pathway mutation status, as well as tumor mutation burden (TMB)\n- Protein plots similar to cBioPortal oncoprints or lollipop plots\n\n\n## Authors\n\n- Christian Brueffer ([@cbrueffer](http://github.com/cbrueffer/))\n- Sergii Gladchuk ([@sergiigladchuk](http://github.com/sergiigladchuk/))\n\nThis software was developed as part of a PhD research project in the\n[laboratory of Lao H. Saal, Translational Oncogenomics Unit, Department of Oncology and Pathology, Lund University, Sweden](https://www.med.lu.se/saalgroup).\n\n\n## Availability\n\nA MutationExplorer instance with the data from 3,217 primary breast tumor transcriptomes from the [Sweden Cancerome Analysis Network--Breast (SCAN-B)](https://portal.research.lu.se/portal/en/projects/sweden-cancerome-analysis-network--breast-scanb-a-largescale-multicenter-infrastructure-towards-implementation-of-breast-cancer-genomic-analyses-in-the-clinical-routine%2898b7c09f-85d5-4f98-bcae-a43bffb6f869%29/publications.html) can be accessed at https://oncogenomics.bmc.lu.se/MutationExplorer.\n\n\n## Citation\n\nBrueffer *et al* (2020). The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome. EMBO Molecular Medicine, 12(10):e12118. DOI: [10.15252/emmm.202012118](https://doi.org/10.15252/emmm.202012118)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbrueffer%2Fmutationexplorer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbrueffer%2Fmutationexplorer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbrueffer%2Fmutationexplorer/lists"}