{"id":21023861,"url":"https://github.com/biogenies/imputomics","last_synced_at":"2025-05-15T08:33:03.087Z","repository":{"id":181790864,"uuid":"582726323","full_name":"BioGenies/imputomics","owner":"BioGenies","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-07T08:27:41.000Z","size":11359,"stargazers_count":10,"open_issues_count":6,"forks_count":3,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-05-10T03:08:55.273Z","etag":null,"topics":["amputation","imputation","metabolomics","missing-values","shiny","webserver"],"latest_commit_sha":null,"homepage":"http://biogenies.info/imputomics/","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/BioGenies.png","metadata":{"files":{"readme":"README.Rmd","changelog":"CHANGELOG","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":"2022-12-27T17:40:04.000Z","updated_at":"2024-08-23T16:48:15.000Z","dependencies_parsed_at":"2023-12-21T12:12:03.140Z","dependency_job_id":"ca7bec54-f2bb-44c4-9076-cb60160bcf80","html_url":"https://github.com/BioGenies/imputomics","commit_stats":null,"previous_names":["biogenies/imputomics"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Fimputomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/imputomics/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254304668,"owners_count":22048447,"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":["amputation","imputation","metabolomics","missing-values","shiny","webserver"],"created_at":"2024-11-19T11:20:14.183Z","updated_at":"2025-05-15T08:32:58.074Z","avatar_url":"https://github.com/BioGenies.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n\n# imputomics \u003cimg src='man/figures/logo.png' align=\"right\" height=\"150\"/\u003e\n\n*imputomics* is an R package and a shiny web server designed to simulate\nand impute missing values. It offers 42 algorithms for imputing missing\nvalues, especially in different types of ‘-omics’ data such as genomics,\ntranscriptomics, proteomics, and metabolomics. imputomics provides a\nuser-friendly interface that allows users to simulate missing values\nbased on different distributions and impute missing values using\nstate-of-the-art methods.\n\n## Key Features:\n\n1.  Imputation methods: imputomics offers the biggest collection of\n    imputation methods for different types of omics data, including\n    k-nearest neighbors (KNN), random forests, expectation-maximization\n    (EM) algorithm, and principal components analysis (PCA) and many\n    others.\n\n2.  Performance evaluation: imputomics facilitates evaluating the\n    performance of imputation methods. Users can evaluate imputation\n    accuracy and compare different methods using metrics such as root\n    mean squared error (RMSE), mean absolute error (MAE), and\n    coefficient of determination (R-squared).\n\n3.  Simulation of missing values: imputomics provides a variety of\n    options for simulating missing values, including missing completely\n    at random (MCAR), missing at random (MAR), and missing not at random\n    (MNAR) mechanisms. Users can specify the percentage of missing\n    values and the distribution from which the missing values are\n    generated.\n    \n\n\n# Getting started\n\nThis repository contains the data and code necessary to reproduce the\nresults from the paper *imputomics: comprehensive missing data\nimputation for metabolomics data*. It uses\n[renv](https://CRAN.R-project.org/package=renv) package to assure the\nreproducibility. As *imputomics* implements lots of missing value\nimputations methods from other R packages.\n\n## Webserver\n\nThe *imputomics* can be accessed through our [web\nserver](http://imputomics.umb.edu.pl/).\n\n## Installation\n\n*imputomics* is available on\n[GitHub](https://github.com/BioGenies/imputomics)\n\nTo install *imputomics* you need to have *R* version \u003e= 4.2.0.\n\n``` r\ndevtools::install_github(\"BioGenies/imputomics\")\n```\n\nSometimes, not all packages can be installed on the first try. In this case, consider re-running the *install_github* function. \n\n### Docker\n\nTo enhance the reproducibility of *imputomics*, we share it also as a [rocker-based](https://github.com/rocker-org) container. The docker manifest is available in the *imputomics* repository: https://github.com/BioGenies/imputomics/blob/main/Dockerfile_imputomics.\n\n\n## Reproducibility\n\nTo reproduce our environment you need to git clone our repo and activate renv.\n\n``` bash \ngit clone https://github.com/BioGenies/imputomics.git\n```\n``` r\nrenv::activate()\nrenv::restore()\n```\n\n### Troubleshooting\n\nQ: I am receiving the following error message: \"Error: HTTP error 403. API rate limit exceeded for [my IP]\".\nA: Due to its comprehensiveness, *imputomics* downloads many packages from GitHub, which may lead to exceeding the limit of GitHub API queries. \nPlease consider setting the GitHub API token with usethis::create_github_token().\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","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Fimputomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Fimputomics/lists"}