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returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["enrichment","generalized-linear-models","logistic-regression","methylation","ontology","shiny"],"created_at":"2025-10-20T14:18:59.320Z","updated_at":"2026-02-21T10:31:34.440Z","avatar_url":"https://github.com/reese3928.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"methylGSA\n===========\n\n`methylGSA` is a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. \n\nThe Bioconductor package can be found [here](https://bioconductor.org/packages/release/bioc/html/methylGSA.html).    \nThe Bioconductor package vignette can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/methylGSA/inst/doc/methylGSA-vignette.html).   \nThe `methylGSA` paper can be found [here](https://doi.org/10.1093/bioinformatics/bty892).\n\nShiny app installation\n------------\nThe following packages are required to be installed before launching the app.    \nPackages from CRAN:\n```{r}    \ninstall.packages(\"DT\")    \ninstall.packages(\"ggplot2\")       \ninstall.packages(\"shinycssloaders\")     \n```\n\nPackages from Bioconductor:    \nIf analyzing 450K array, `IlluminaHumanMethylation450kanno.ilmn12.hg19` needs to be installed.\n```{r}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) install.packages(\"BiocManager\")\nBiocManager::install(\"IlluminaHumanMethylation450kanno.ilmn12.hg19\")\n```\nIf analyzing EPIC array, `IlluminaHumanMethylationEPICanno.ilm10b4.hg19` needs to be installed.\n```{r}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) install.packages(\"BiocManager\")\nBiocManager::install(\"IlluminaHumanMethylationEPICanno.ilm10b4.hg19\")\n```\n\nLaunch the app\n------------\nAfter installation, the app can be launched with the following code:\n```{r}\nlibrary(methylGSA)\nmethylGSA::runExample()\n```\n\nStep-by-step instructions\n------------\nA step-by-step instructions on the workflow of the app can be found [here](https://github.com/reese3928/methylGO-RShiny-app/raw/master/instructions.pdf).\n\nCitation\n------------\nRen, X., \u0026 Kuan, P. F. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics, 35(11), 1958-1959.\n\n@article{ren2019methylgsa,    \ntitle={methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing},    \nauthor={Ren, Xu and Kuan, Pei Fen},    \njournal={Bioinformatics},    \nvolume={35},    \nnumber={11},    \npages={1958--1959},    \nyear={2019},    \npublisher={Oxford University Press}    \n}\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freese3928%2Fmethylgsa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freese3928%2Fmethylgsa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freese3928%2Fmethylgsa/lists"}