{"id":21673804,"url":"https://github.com/openmendel/mendelestimatefrequencies.jl","last_synced_at":"2025-03-20T08:42:45.761Z","repository":{"id":104909588,"uuid":"63363030","full_name":"OpenMendel/MendelEstimateFrequencies.jl","owner":"OpenMendel","description":"This analysis option calculates a likelihood-based estimate of allele frequencies.","archived":false,"fork":false,"pushed_at":"2019-09-11T15:42:39.000Z","size":67,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-01-25T09:42:09.720Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Julia","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/OpenMendel.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":"2016-07-14T19:15:53.000Z","updated_at":"2019-09-11T15:42:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"5437ee52-03cf-49ec-b51c-54dd7c4adf15","html_url":"https://github.com/OpenMendel/MendelEstimateFrequencies.jl","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/OpenMendel%2FMendelEstimateFrequencies.jl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelEstimateFrequencies.jl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelEstimateFrequencies.jl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelEstimateFrequencies.jl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenMendel","download_url":"https://codeload.github.com/OpenMendel/MendelEstimateFrequencies.jl/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244583048,"owners_count":20476233,"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":"2024-11-25T13:41:23.598Z","updated_at":"2025-03-20T08:42:45.724Z","avatar_url":"https://github.com/OpenMendel.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MendelEstimateFrequencies\n\nThis [Julia](http://julialang.org/) package calculates a likelihood-based estimate of allele frequencies. MendelEstimateFrequencies is one component of the umbrella [OpenMendel](https://openmendel.github.io) project.\n\n[![](https://img.shields.io/badge/docs-current-blue.svg)](https://OpenMendel.github.io/MendelEstimateFrequencies.jl)\n\n## Installation\n\n*Note: The three OpenMendel packages (1) [SnpArrays](https://openmendel.github.io/SnpArrays.jl/latest/), (2) [MendelSearch](https://openmendel.github.io/MendelSearch.jl), and (3) [MendelBase](https://openmendel.github.io/MendelBase.jl) must be installed before any other OpenMendel package will run. It is easiest if these three packages are installed in the above order and before any other OpenMendel package.*\n\nWithin Julia, use the package manager to install MendelEstimateFrequencies:\n\n    pkg\u003e add https://github.com/OpenMendel/MendelEstimateFrequencies.jl\n\nThis package supports Julia v1.0+\n\n## Data Files\n\nTo run this analysis package you will need to prepare a Control file and have your data files available. The Control file holds the names of your data files and any optional parameters for the analysis. Details on the general format and contents of the Control and data files can be found on the MendelBase [documentation page](https://openmendel.github.io/MendelBase.jl). Descriptions of the specific options available within the MendelEstimateFrequencies analysis package are in the MendelEstimateFrequencies [documentation page](https://openmendel.github.io/MendelEstimateFrequencies.jl).\n\nThere are example data files in the \"data\" subfolder of each Mendel package.\n\n## Running the Analysis\n\nTo run this analysis package, first launch Julia. Then load the package with the command:\n\n     julia\u003e using MendelEstimateFrequencies\n\nNext, if necessary, change to the directory containing your files, for example,\n\n     julia\u003e cd(\"~/path/to/data/files/\")\n\nFinally, to run the analysis using the parameters in the control file Control_file.txt use the command:\n\n     julia\u003e EstimateFrequencies(\"Control_file.txt\")\n\n*Note: The package is called* MendelEstimateFrequencies *but the analysis function is called simply* EstimateFrequencies.\n\n## Citation\n\nIf you use this analysis package in your research, please cite the following reference in the resulting publications:\n\n*OPENMENDEL: a cooperative programming project for statistical genetics. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. Hum Genet. 2019 Mar 26. doi: 10.1007/s00439-019-02001-z. [Epub ahead of print] PMID: 30915546*\n\n*Lange K, Sinsheimer JS, Sobel E (2005). Association testing with Mendel. Genetic Epidemiology 29:36-50.*\n\n\u003c!--- ## Contributing\nWe welcome contributions to this Open Source project. To contribute, follow this procedure ... ---\u003e\n\n## Acknowledgments\n\nThis project is supported by the National Institutes of Health under NIGMS awards R01GM053275 and R25GM103774 and NHGRI award R01HG006139.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenmendel%2Fmendelestimatefrequencies.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenmendel%2Fmendelestimatefrequencies.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenmendel%2Fmendelestimatefrequencies.jl/lists"}