{"id":21023881,"url":"https://github.com/biogenies/imputomics-ws","last_synced_at":"2026-02-16T13:04:29.640Z","repository":{"id":183678968,"uuid":"670544633","full_name":"BioGenies/imputomics-ws","owner":"BioGenies","description":null,"archived":false,"fork":false,"pushed_at":"2024-05-16T12:58:57.000Z","size":21,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-10-08T13:44:17.820Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://biogenies.info/imputomics-ws/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioGenies.png","metadata":{"files":{"readme":"README.Rmd","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":"2023-07-25T09:38:42.000Z","updated_at":"2023-07-25T10:32:58.000Z","dependencies_parsed_at":"2025-01-20T13:43:08.285Z","dependency_job_id":"a3faf3e6-a511-4bf3-a1dc-032185096d0c","html_url":"https://github.com/BioGenies/imputomics-ws","commit_stats":null,"previous_names":["biogenies/imputomics-ws"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BioGenies/imputomics-ws","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics-ws","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics-ws/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics-ws/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics-ws/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/imputomics-ws/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics-ws/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29508741,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-16T09:05:14.864Z","status":"ssl_error","status_checked_at":"2026-02-16T08:55:59.364Z","response_time":115,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-11-19T11:20:45.525Z","updated_at":"2026-02-16T13:04:29.623Z","avatar_url":"https://github.com/BioGenies.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"---\n  output: github_document\n---\n\n# imputomics\n\nImputomics is a software package  and a web server designed to simulate and impute \nmissing values in omics datasets. It is a comprehensive package that offers a range \nof methods for simulating and imputing missing values in different types of omics \ndata such as genomics, transcriptomics, proteomics, and metabolomics. Imputomics \nprovides a user-friendly interface that allows users to simulate missing values \nbased on different distributions and impute missing values using state-of-the-art \nmethods. \n\n## Key Features:\n\n1. Simulation of missing values: Imputomics provides a variety of options for simulating \nmissing values, including missing completely at random (MCAR), missing at random (MAR), \nand missing not at random (MNAR) mechanisms. Users can specify the percentage of \nmissing values and the distribution from which the missing values are generated.\n\n2. Imputation methods: Imputomics offers the biggest collection of imputation \nmethods for different types of omics data, including k-nearest neighbors (KNN), \nrandom forests, expectation-maximization (EM) algorithm, and principal components\nanalysis (PCA) and many others. \n\n3. Performance evaluation: Imputomics facilitates evaluating the performance of \nimputation methods. Users can evaluate imputation accuracy and compare different \nmethods using metrics such as root mean squared error (RMSE), mean absolute \nerror (MAE), and coefficient of determination (R-squared).\n\n\n\n# Getting started\n\n\nThis repository contains the data and code necessary to reproduce the results from the paper *Imputomics: comprehensive missing data imputation for metabolomics data*. It uses [renv](https://CRAN.R-project.org/package=renv) package to assure the reproducibility. As *imputomics* implements lots of missing value imputations methods from other R packages.\n\n## Webserver\n\nThe *imputomics* can be accessed through our [web server](http://imputomics.umb.edu.pl/).\n\n## Installation\n\n*imputomics* is available on [GitHub](https://github.com/BioGenies/imputomics)\n\n```R\ndevtools::install_github(\"michbur/imputomics\")\nrenv::restore()\n```\n\n## Run imputomics\n\nTo run *imputomics* type the following command into an R console.\n\n```R\nimputomics::imputomics_gui()\n```\n\n\u003c!-- # How to cite --\u003e\n\n```{r echo = FALSE, results = 'asis'}\nsource(system.file(\"readme_scripts.R\", package = \"imputomics\"))\ncat(imputomics_citation())\ncat(imputomics_contact())\ncat(imputomics_funding())\ncat(imputomics_funding_images())\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fimputomics-ws","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Fimputomics-ws","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fimputomics-ws/lists"}