{"id":19749599,"url":"https://github.com/mskcc/msisensor","last_synced_at":"2026-05-11T13:07:40.817Z","repository":{"id":75108450,"uuid":"318580128","full_name":"mskcc/msisensor","owner":"mskcc","description":null,"archived":false,"fork":false,"pushed_at":"2020-12-04T16:55:50.000Z","size":49507,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-02-28T08:28:47.472Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","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/mskcc.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-12-04T16:55:17.000Z","updated_at":"2025-02-14T17:54:54.000Z","dependencies_parsed_at":null,"dependency_job_id":"f208f777-b550-459f-84d4-80a2a3c9ca14","html_url":"https://github.com/mskcc/msisensor","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/msisensor","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fmsisensor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fmsisensor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fmsisensor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fmsisensor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/msisensor/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fmsisensor/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32896005,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-10T13:40:02.631Z","status":"online","status_checked_at":"2026-05-11T02:00:05.975Z","response_time":120,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-12T02:27:23.400Z","updated_at":"2026-05-11T13:07:40.801Z","avatar_url":"https://github.com/mskcc.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"***Note:* For questions and discussion about [msisensor](https://github.com/ding-lab/msisensor), please visit the repository of [msisensor-pro](https://github.com/xjtu-omics/msisensor-pro) at https://github.com/xjtu-omics/msisensor-pro.**\n\n\n\n## MSIsensor\n\n\n\n**MSIsensor** is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. Given paired tumor and normal sequence data, it builds a distribution for expected (normal) and observed (tumor) lengths of repeated sequence per microsatellite, and compares them using Pearson's Chi-Squared Test. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving microsatellite instability (MSI) status from standard tumor-normal paired sequence data. MSIsensor is publiched in [*Bioinformatics*](https://www.ncbi.nlm.nih.gov/pubmed/24371154). Please click [here](https://github.com/ding-lab/msisensor/blob/master/README_msisensor.md) to see more details about MSIsensor. If you have any questions about MSIsensor, please contact one or more of the following folks:\nBeifang Niu (\u003cbniu@sccas.cn\u003e), Kai Ye (\u003ckaiye@xjtu.edu.cn\u003e) or Li Ding (\u003clding@wustl.edu\u003e).\n\nIf you used this tool for your work, please cite [PMID 24371154](https://www.ncbi.nlm.nih.gov/pubmed/24371154)\n\n\n**[MSIsensor-pro](https://github.com/xjtu-omics/msisensor-pro)** is a new MSI detection method developed by [Kai Ye](http://gr.xjtu.edu.cn/web/kaiye/english)  et al. [MSIsensor-pro](https://github.com/xjtu-omics/msisensor-pro) is a fast, accurate, and matched-normal-sample-free MSI detection method. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. **[MSIsensor-pro](https://github.com/xjtu-omics/msisensor-pro)** is now published in [*Genomics Proteomics \u0026 Bioinformatics*](https://www.sciencedirect.com/science/article/pii/S1672022920300218). If you have any question about MSIsensor-pro, please [open a issue](https://github.com/xjtu-omics/msisensor-pro/issues/new) on [MSIsensor-pro's homepage](https://github.com/xjtu-omics/msisensor-pro) or contact with Kai Ye (kaiye@xjtu.edu.cn) directly. \n\n\n**MSIsensor2** is also a MSI detecteion method specially designed for tumor only sequencing data. MSIsensor2 was developed by Beifang Niu's lab (bniu@sccas.cn) independently. Please try the MSIsensor2 here: https://github.com/niu-lab/msisensor2 or require any further details here: http://niulab.scgrid.cn/msisensor2/index.html.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fmsisensor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fmsisensor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fmsisensor/lists"}