{"id":19857036,"url":"https://github.com/griffithlab/genvisr-1","last_synced_at":"2026-06-08T18:31:24.042Z","repository":{"id":78129780,"uuid":"50870347","full_name":"griffithlab/GenVisR-1","owner":"griffithlab","description":"This is a read-only mirror of the Bioconductor SVN repository. 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GenVisr (Genomic Visualizations in R) attempts to alleviate this burden by providing highly customizable publication-quality graphics focused primarily on a cohort level (i.e., multiple samples/patients). GenVisr attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.\n\n## Installation Instructions\n\nNote requires R \u003e= 3.2.1, see Description file for a full list of dependencies\n\n* Install devtools\n```R\ninstall.packages(\"devtools\")\n```\n\n* Install Bioconductor dependencies\n```R\nsource(\"http://bioconductor.org/biocLite.R\")\nbiocLite(c(\"AnnotationDbi\", \"biomaRt\", \"Biostrings\", \"GenomicFeatures\", \"GenomicRanges\", \"Rsamtools\"))\n```\n\n* It is suggested but not required to install knitr and rmarkdown for vignette creation\n```R\ninstall.packages(c(\"rmarkdown\", \"knitr\"))\n```\n\n* Install GenVisR\n```R\ndevtools::install_github(\"griffithlab/GenVisR\")\n```\n\n## Tips for developers\n* It is recommended to use Rstudio for development, Clone the repo and open the \"GGgenome.Rproj\" folder in Rstudio.\n* It is necessary to manual install all packages (since you are cloning and building, not installing), all packages within the imports, Depends, and Suggests flags in the \"DESCRIPTION\" file (~/GenVisR/DESCRIPTION) should be installed! The r-package devtools should be installed as well!\n* Build and Reload the package at this step (shorcut: Shift+Cmd+B)\n* GenVisR uses roxygen2 for documentation, to update the Reference Manuscript edit the roxygen2 flags (i.e. @param, @details, etc.) in the code. These are within the R function files in ~/GenVisR/R/, Then run devtools::document().\n* To update the vignette edit the R markdown file in the vignettes subdirectory (~/GenVisR/vignettes/GenVisR_intro.Rmd) and press the knit button in Rstudio\n* Code for GenVisR is within the R subdirectory (~/GenVisR/R/), make changes there. Be sure to build and reload the package from Rstudio to test changes (Rstudio -\u003e Build -\u003e Build \u0026 Reload || Shift+CMD+B)\n* test cases are in the test subdirectory (~/GenVisR/tests/testthat/), tests must be named with the character string \"test\" in the beginning of the name (i.e. for the waterfall function the test file would look like test-waterfall.R). To run tests run devtools::test()\n\n[![Coverage Status](https://coveralls.io/repos/griffithlab/GenVisR/badge.svg?branch=master\u0026service=github)](https://coveralls.io/github/griffithlab/GenVisR?branch=master)\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fgenvisr-1","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fgenvisr-1","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fgenvisr-1/lists"}