{"id":21583180,"url":"https://github.com/tnaake/matrixqcvis","last_synced_at":"2025-04-10T18:54:22.695Z","repository":{"id":48184510,"uuid":"346692374","full_name":"tnaake/MatrixQCvis","owner":"tnaake","description":null,"archived":false,"fork":false,"pushed_at":"2024-04-12T13:32:30.000Z","size":4683,"stargazers_count":5,"open_issues_count":2,"forks_count":1,"subscribers_count":2,"default_branch":"devel","last_synced_at":"2024-04-12T15:06:31.172Z","etag":null,"topics":["metabolomics","proteomics","qc","r","shiny","transcriptomics","visualization"],"latest_commit_sha":null,"homepage":"","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/tnaake.png","metadata":{"files":{"readme":"README.md","changelog":null,"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}},"created_at":"2021-03-11T12:20:18.000Z","updated_at":"2024-04-23T12:41:05.892Z","dependencies_parsed_at":"2024-04-02T14:28:11.570Z","dependency_job_id":"85e228d2-7a43-426f-93ec-57994bb655af","html_url":"https://github.com/tnaake/MatrixQCvis","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/tnaake%2FMatrixQCvis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMatrixQCvis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMatrixQCvis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tnaake%2FMatrixQCvis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tnaake","download_url":"https://codeload.github.com/tnaake/MatrixQCvis/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248275504,"owners_count":21076609,"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":["metabolomics","proteomics","qc","r","shiny","transcriptomics","visualization"],"created_at":"2024-11-24T14:18:28.709Z","updated_at":"2025-04-10T18:54:22.672Z","avatar_url":"https://github.com/tnaake.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# _MatrixQCvis_ - Interactive exploration of data quality\r\n\r\n## Overview\r\n\r\nThe _MatrixQCvis_ package provides shiny-based interactive visualization of \r\ndata quality metrics at the per-sample and per-feature level. It is broadly \r\napplicable to quantitative omics data types that come in matrix-like format \r\n(features x samples). It enables the detection of low-quality samples, drifts, \r\noutliers and batch effects in data sets. Visualizations include amongst \r\nothers bar- and violin plots of the (count/intensity) values, mean vs standard \r\ndeviation plots, MA plots, empirical cumulative distribution function (ECDF) \r\nplots, visualizations of the distances between samples, and multiple types of \r\ndimension reduction plots. \r\n\r\nFurthermore, _MatrixQCvis_ allows for differential expression analysis based \r\non the _limma_ (moderated t-tests) and _proDA_ (Wald tests) packages. \r\n_MatrixQCvis_ builds upon the popular Bioconductor _SummarizedExperiment_ \r\nS4 class and enables thus the facile integration into existing workflows. \r\n\r\nThe package is especially tailored towards metabolomics and proteomics mass \r\nspectrometry data, but also allows to assess the data quality of other data \r\ntypes that can be represented in a _SummarizedExperiment_ object.\r\n\r\n## Installation\r\n\r\nTo install _MatrixQCvis_ from GitHub, install the package via `devtools`:\r\n```r \r\nif (!requireNamespace(\"devtools\", quietly = TRUE))\r\n    install.packages(\"devtools\")\r\nlibrary(devtools)\r\ninstall_github(\"tnaake/MatrixQCvis\")\r\n```\r\n\r\nAlternatively, the _MatrixQCvis_ package can also be installed via the \r\nBioconductor project. \r\n\r\nFor the [release](http://bioconductor.org/packages/release/bioc/html/MatrixQCvis.html) \r\nversion enter:\r\n\r\n```r\r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\r\n    install.packages(\"BiocManager\")\r\nBiocManager::install(\"MatrixQCvis\")\r\n```\r\n\r\nFor the [development](http://bioconductor.org/packages/devel/bioc/html/MatrixQCvis.html) \r\nversion enter:\r\n```r\r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\r\n    install.packages(\"BiocManager\")\r\n\r\n# the following initializes usage of Bioc devel\r\nBiocManager::install(version = \"devel\")\r\n\r\nBiocManager::install(\"MatrixQCvis\")\r\n```\r\n\r\nThe version at the Bioconductor development branch and the code in the Github repository \r\nare places where we publicly disclose our development process and users are \r\nsupposed to refer to the Bioconductor releae version as the authoritative version for \r\nuse.\r\n\r\n## Quick start\r\n\r\n_MatrixQCvis_ is based on the _SummarizedExperiment_ class. The shiny \r\napplication can be started with passing a _SummarizedExperiment_ object \r\n(in the following denoted as _se_) or without such an object. The \r\nsecond function call will load an interface to load a \r\n_SummarizedExperiment_ object stored in a RDS file. \r\n\r\n```r\r\nlibrary(\"MatrixQCvis\")\r\n\r\n## initialize the application with passing a SummarizedExperiment object\r\nshinyQC(se)\r\n\r\n## initialize the application without passing a SummarizedExperiment object\r\nshinyQC()\r\n```\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftnaake%2Fmatrixqcvis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftnaake%2Fmatrixqcvis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftnaake%2Fmatrixqcvis/lists"}