{ "_id": "6a1ac1581d7bb097a09d820b", "Package": "omicsViewer", "Title": "Interactive and explorative visualization of\nSummarizedExperssionSet or ExpressionSet using omicsViewer", "Version": "1.17.0", "Authors@R": "person(\"Chen\", \"Meng\", email = \"mengchen18@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Description": "omicsViewer visualizes ExpressionSet (or\nSummarizedExperiment) in an interactive way. The omicsViewer\nhas a separate back- and front-end. In the back-end, users need\nto prepare an ExpressionSet that contains all the necessary\ninformation for the downstream data interpretation. Some extra\nrequirements on the headers of phenotype data or feature data\nare imposed so that the provided information can be clearly\nrecognized by the front-end, at the same time, keep a minimum\nmodification on the existing ExpressionSet object. The pure\ndependency on R/Bioconductor guarantees maximum flexibility in\nthe statistical analysis in the back-end. Once the\nExpressionSet is prepared, it can be visualized using the\nfront-end, implemented by shiny and plotly. Both features and\nsamples could be selected from (data) tables or graphs (scatter\nplot/heatmap). Different types of analyses, such as enrichment\nanalysis (using Bioconductor package fgsea or fisher's exact\ntest) and STRING network analysis, will be performed on the fly\nand the results are visualized simultaneously. When a subset of\nsamples and a phenotype variable is selected, a significance\ntest on means (t-test or ranked based test; when phenotype\nvariable is quantitative) or test of independence (chi-square\nor fisher’s exact test; when phenotype data is categorical)\nwill be performed to test the association between the phenotype\nof interest with the selected samples. Additionally, other\nanalyses can be easily added as extra shiny modules. Therefore,\nomicsViewer will greatly facilitate data exploration, many\ndifferent hypotheses can be explored in a short time without\nthe need for knowledge of R. In addition, the resulting data\ncould be easily shared using a shiny server. Otherwise, a\nstandalone version of omicsViewer together with designated\nomics data could be easily created by integrating it with\nportable R, which can be shared with collaborators or submitted\nas supplementary data together with a manuscript.", "License": "GPL-2", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "biocViews": "Software, Visualization, GeneSetEnrichment,\nDifferentialExpression, MotifDiscovery, Network,\nNetworkEnrichment", "BugReports": "https://github.com/mengchen18/omicsViewer", "URL": "https://github.com/mengchen18/omicsViewer", "Video": "https://www.youtube.com/watch?v=0nirB-exquY&list=PLo2m88lJf-RRoLKMY8UEGqCpraKYrX5lk", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libjpeg-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:21 UTC", "RemoteUrl": "https://github.com/bioc/omicsViewer", "RemoteRef": "HEAD", "RemoteSha": 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