{"id":13470161,"url":"https://github.com/abodein/timeOmics","last_synced_at":"2025-03-26T11:30:45.748Z","repository":{"id":124275577,"uuid":"210380101","full_name":"abodein/timeOmics","owner":"abodein","description":"Time-Course Multi-Omics data integration","archived":false,"fork":false,"pushed_at":"2024-04-09T19:32:33.000Z","size":3829,"stargazers_count":24,"open_issues_count":0,"forks_count":6,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-10-30T01:58:11.422Z","etag":null,"topics":["cluster","integration","multi-omics","time-series"],"latest_commit_sha":null,"homepage":"","language":"R","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/abodein.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","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":"2019-09-23T14:44:59.000Z","updated_at":"2024-08-29T07:38:07.000Z","dependencies_parsed_at":"2024-04-09T20:37:40.662Z","dependency_job_id":"76354c73-c1b1-4a59-8381-dadfb626da37","html_url":"https://github.com/abodein/timeOmics","commit_stats":{"total_commits":126,"total_committers":4,"mean_commits":31.5,"dds":"0.11904761904761907","last_synced_commit":"1436210cf5eaa51fead055676643da0d952988f4"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abodein%2FtimeOmics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abodein%2FtimeOmics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abodein%2FtimeOmics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abodein%2FtimeOmics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/abodein","download_url":"https://codeload.github.com/abodein/timeOmics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245644239,"owners_count":20649159,"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":["cluster","integration","multi-omics","time-series"],"created_at":"2024-07-31T16:00:24.211Z","updated_at":"2025-03-26T11:30:44.913Z","avatar_url":"https://github.com/abodein.png","language":"R","funding_links":[],"categories":["Software packages and methods"],"sub_categories":["Longitudinal Multi-omics Integration"],"readme":"\n[![Build Status](https://travis-ci.com/abodein/timeOmics_BioC.svg?branch=master)](https://travis-ci.com/abodein/timeOmics)\n[![codecov](https://codecov.io/gh/abodein/timeOmics_BioC/branch/master/graph/badge.svg)](https://codecov.io/gh/abodein/timeOmics)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n# timeOmics\n\n***timeOmics*** is a generic data-driven framework to integrate multi-Omics longitudinal data (**A.**) measured on the same biological samples and select key temporal features with strong associations within the same sample group.\n\n![](./man/figures/method_overview.png)\n\nThe main steps of ***timeOmics*** are:\n\n* a pre-processing step (**B.**) Normalize and filter low-expressed features, except those not varying over time,\n* a modelling step (**C.**)  Capture inter-individual variability in biological/technical replicates and accommodate heterogeneous experimental designs,\n* a clustering step (**D.**) Group features with the same expression profile over time. Feature selection step can also be used to identify a signature per cluster,\n* a post-hoc validation step (**E.**) Ensure clustering quality.\n\n***timeOmics*** can be applied on both single-Omic or multi-Omics experimental design.\n\n*\u003cfont color=\"green\"\u003e If you came to this page thanks to our article and you wish to access its example scripts please follow this\n\u003ca href=\"https://github.com/abodein/timeOmics_frontiers\"\u003e link \u003c/a\u003e.\u003c/font\u003e*\n\n## Installation\n\n### Latest `GitHub` Version\n\nInstall the devtools package in R, then load it and install the latest stable version of `timeOmics` from `GitHub`\n\n```r\n## install devtools if not installed\nif (!requireNamespace(\"devtools\", quietly = TRUE))\n    install.packages(\"devtools\")\n## install timeOmics\ndevtools::install_github(\"abodein/timeOmics\")\n```\n\n## Citing\n\n*Bodein A, Chapleur O, Droit A and Lê Cao K-A (2019) A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types. Front. Genet. 10:963. \u003ca href=\"http://dx.doi.org/10.3389/fgene.2019.00963\"\u003e doi:10.3389/fgene.2019.00963\u003c/a\u003e*\n\n## Maintainer\nAntoine Bodein (\u003cantoine.bodein.1@ulaval.ca\u003e)\n\n## Bugs/Feature requests\n\nIf you have any bugs or feature requests, [let us know](https://github.com/abodein/timeOmics_BioC/issues). Thanks!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabodein%2FtimeOmics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabodein%2FtimeOmics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabodein%2FtimeOmics/lists"}