{"id":14068015,"url":"https://github.com/umr1283/CARoT","last_synced_at":"2025-07-30T02:32:41.308Z","repository":{"id":132188678,"uuid":"181004724","full_name":"umr1283/CARoT","owner":"umr1283","description":"Centralised and Automated RepOrting Tools","archived":true,"fork":false,"pushed_at":"2021-09-15T22:03:50.000Z","size":2720,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-12-04T08:36:57.987Z","etag":null,"topics":["omics","quality-control","r","r-package","r-stats","reporting"],"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/umr1283.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-04-12T12:34:23.000Z","updated_at":"2023-01-27T23:59:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"bd0102b2-aa16-45d5-bc2d-ef83c79ae7bd","html_url":"https://github.com/umr1283/CARoT","commit_stats":null,"previous_names":[],"tags_count":37,"template":false,"template_full_name":null,"purl":"pkg:github/umr1283/CARoT","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/umr1283%2FCARoT","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/umr1283%2FCARoT/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/umr1283%2FCARoT/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/umr1283%2FCARoT/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/umr1283","download_url":"https://codeload.github.com/umr1283/CARoT/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/umr1283%2FCARoT/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267798625,"owners_count":24145727,"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","status":"online","status_checked_at":"2025-07-30T02:00:09.044Z","response_time":70,"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":["omics","quality-control","r","r-package","r-stats","reporting"],"created_at":"2024-08-13T07:05:53.891Z","updated_at":"2025-07-30T02:32:41.018Z","avatar_url":"https://github.com/umr1283.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\n# Centralised and Automated Reporting Tools \u003cimg src=\"man/figures/carot.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: retired](https://img.shields.io/badge/lifecycle-retired-red.svg)](https://github.com/umr1283/CARoT)\n[![GitHub tag](https://img.shields.io/github/tag/umr1283/CARoT.svg?label=latest tag\u0026include_prereleases)](https://github.com/umr1283/CARoT)\n[![R build status](https://github.com/umr1283/CARoT/workflows/R-CMD-check/badge.svg)](https://github.com/umr1283/CARoT/actions)\n\u003c!-- badges: end --\u003e\n\n## Installation\n\n```{r, eval = FALSE}\n# Install CARoT from CRAN:\ninstall.packages(\"CARoT\")\n\n# Or the the development version from GitHub:\n# install.packages(\"remotes\")\nremotes::install_github(\"umr1283/CARoT\")\n```\n```{r}\nlibrary(CARoT)\n```\n\n## Overview \n\n*CARoT* (Centralised and Automated Reporting Tools) is an under development set of Quality-Control reporting tools and some other functions.\n\nCurrently *CARoT* includes the following functions from other packages:\n\n* [`rain`](https://github.com/umr1283/rain)\n    - `rain::estimate_ethnicity()` allows to format VCF files \n        and compute the genomic components (and some figures) for ethnicity \n        using [flashpca](https://github.com/gabraham/flashpca) software\n    - `rain::pca_report()` allows to compute an analysis report \n        using principal component analysis from \n        [flashpca](https://github.com/gabraham/flashpca) software.  \n\n* [`MiSTr`](https://github.com/mcanouil/MiSTr)\n    - `MiSTr::mist()` allows to test for association between \n    a set of SNPS/genes and continuous or binary outcomes by including variant \n    characteristic information and using (weighted) score statistics.\n\n* [`dgapaq`](https://github.com/umr1283/dgapaq)\n    - `dgapaq::qc_plink()` allows to compute quality-control of genotyping array (PLINK format) \n        using a Rmarkdown template.\n    - `dgapaq::qc_vcf()` allows to compute post-imputation quality-control report \n        using a default Rmarkdown template.\n\n* [`dmapaq`](https://github.com/umr1283/dmapaq)\n    - `dmapaq::ggheatmap()` allows to compute heatmap with dendrogram on x-axis and y-axis \n        using [ggplot2](https://ggplot2.tidyverse.org/).\n    - `dmapaq::read_idats()` allows to efficiently import idats files mostly \n        using [minfi](https://bioconductor.org/packages/minfi/) functions.\n    - `dmapaq::qc_idats()` allows to compute quality-control of methylation array from Illumina \n        using a Rmarkdown template.\n\n## Getting help\n\nIf you encounter a clear bug, please file a minimal reproducible example on [github](https://github.com/umr1283/CARoT/issues).  \nFor questions and other discussion, please contact the package maintainer.\n\n---\n\nPlease note that this project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md).  \nBy participating in this project you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fumr1283%2FCARoT","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fumr1283%2FCARoT","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fumr1283%2FCARoT/lists"}