{"id":17403933,"url":"https://github.com/federicomarini/genetonic","last_synced_at":"2025-04-13T11:48:11.404Z","repository":{"id":36032301,"uuid":"193464295","full_name":"federicomarini/GeneTonic","owner":"federicomarini","description":"Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail","archived":false,"fork":false,"pushed_at":"2025-03-19T15:03:31.000Z","size":126514,"stargazers_count":77,"open_issues_count":19,"forks_count":9,"subscribers_count":4,"default_branch":"devel","last_synced_at":"2025-04-04T05:48:05.821Z","etag":null,"topics":["bioconductor","bioconductor-package","data-exploration","data-visualization","functional-enrichment-analysis","gene-expression","gui","pathway-analysis","r","reproducible-research","rna-seq-analysis","rna-seq-data","shiny","transcriptome","transcriptomics","user-friendly"],"latest_commit_sha":null,"homepage":"https://federicomarini.github.io/GeneTonic","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/federicomarini.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-06-24T08:21:40.000Z","updated_at":"2025-03-07T13:36:53.000Z","dependencies_parsed_at":"2024-09-12T09:09:25.242Z","dependency_job_id":"62993831-9af8-45d9-9aa5-3e945825e670","html_url":"https://github.com/federicomarini/GeneTonic","commit_stats":{"total_commits":1041,"total_committers":7,"mean_commits":"148.71428571428572","dds":"0.025936599423631135","last_synced_commit":"622a3d013d7dd5f92fd563f92e2be8f83f2c7bf2"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/federicomarini%2FGeneTonic","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/federicomarini%2FGeneTonic/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/federicomarini%2FGeneTonic/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/federicomarini%2FGeneTonic/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/federicomarini","download_url":"https://codeload.github.com/federicomarini/GeneTonic/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248710410,"owners_count":21149186,"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":["bioconductor","bioconductor-package","data-exploration","data-visualization","functional-enrichment-analysis","gene-expression","gui","pathway-analysis","r","reproducible-research","rna-seq-analysis","rna-seq-data","shiny","transcriptome","transcriptomics","user-friendly"],"created_at":"2024-10-16T19:09:30.503Z","updated_at":"2025-04-13T11:48:11.382Z","avatar_url":"https://github.com/federicomarini.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003cimg src=\"man/figures/GeneTonic.png\" align=\"right\" alt=\"\" width=\"120\" /\u003e\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# GeneTonic\n\n\u003ca href=\"https://doi.org/10.1186/s12859-021-04461-5\"\u003e\u003cimg src=\"https://img.shields.io/badge/doi-GeneTonic-blue.svg\"\u003e\u003ca\u003e\n\u003ca href=\"https://doi.org/10.1002/cpz1.411\"\u003e\u003cimg src=\"https://img.shields.io/badge/doi-GeneTonic_protocol-blue.svg\"\u003e\u003ca\u003e\n\n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/federicomarini/GeneTonic/workflows/R-CMD-check/badge.svg)](https://github.com/federicomarini/GeneTonic/actions)\n[![](https://bioconductor.org/shields/build/devel/bioc/GeneTonic.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GeneTonic/)\n[![](https://img.shields.io/github/last-commit/federicomarini/GeneTonic.svg)](https://github.com/federicomarini/GeneTonic/commits/master)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)\n[![Codecov.io coverage status](https://codecov.io/github/federicomarini/GeneTonic/coverage.svg?branch=master)](https://codecov.io/github/federicomarini/GeneTonic)\n\u003c!-- badges: end --\u003e\n\nThe goal of GeneTonic is to analyze and integrate the results from Differential Expression analysis and functional enrichment analysis.\n\nThis package provides a Shiny application that aims to combine at different levels the existing pieces of the transcriptome data and results, in a way that makes it easier to generate insightful observations and hypothesis - combining the benefits of interactivity and reproducibility, e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist.\n\nGeneTonic can be found on Bioconductor (https://www.bioconductor.org/packages/GeneTonic).\n\nIf you use GeneTonic in your work, please refer to the original publication :page_facing_up: on BMC Bioinformatics (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5, doi: [10.1186/s12859-021-04461-5](https://doi.org/10.1186/s12859-021-04461-5)).\n\nA preprint :page_facing_up: on GeneTonic is available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1.\n\n## Installation\n\nYou can install the development version of GeneTonic from GitHub with:\n\n```{r eval=FALSE}\nlibrary(\"remotes\")\nremotes::install_github(\"federicomarini/GeneTonic\", \n                        dependencies = TRUE, build_vignettes = TRUE)\n```\n\n## Example\n\nThis is a basic example which shows you how to use `GeneTonic` on a demo dataset (the one included in the `macrophage` package).\n\n```{r eval=FALSE}\nlibrary(\"GeneTonic\")\nexample(\"GeneTonic\")\n\n# which will in the end run\nlibrary(\"macrophage\")\nlibrary(\"DESeq2\")\nlibrary(\"org.Hs.eg.db\")\nlibrary(\"AnnotationDbi\")\n\n# dds object\ndata(\"gse\", package = \"macrophage\")\ndds_macrophage \u003c- DESeqDataSet(gse, design = ~line + condition)\nrownames(dds_macrophage) \u003c- substr(rownames(dds_macrophage), 1, 15)\ndds_macrophage \u003c- estimateSizeFactors(dds_macrophage)\n\n# annotation object\nanno_df \u003c- data.frame(\n  gene_id = rownames(dds_macrophage),\n  gene_name = mapIds(org.Hs.eg.db,\n                     keys = rownames(dds_macrophage),\n                     column = \"SYMBOL\",\n                     keytype = \"ENSEMBL\"),\n  stringsAsFactors = FALSE,\n  row.names = rownames(dds_macrophage)\n)\n\n# res object\ndata(res_de_macrophage, package = \"GeneTonic\")\nres_de \u003c- res_macrophage_IFNg_vs_naive\n\n# res_enrich object\ndata(res_enrich_macrophage, package = \"GeneTonic\")\nres_enrich \u003c- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)\n\nGeneTonic(dds = dds_macrophage,\n          res_de = res_de,\n          res_enrich = res_enrich,\n          annotation_obj = anno_df,\n          project_id = \"my_first_genetonic\")\n```\n\n## Usage overview\n\nYou can find the rendered version of the documentation of `GeneTonic` at the project website https://federicomarini.github.io/GeneTonic, created with `pkgdown`.\n\n## Sneak peek?\n\nPlease visit http://shiny.imbei.uni-mainz.de:3838/GeneTonic/ to see a small demo instance running, on the `macrophage` dataset.\n\n## Development\n\nIf you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an [issue](https://github.com/federicomarini/GeneTonic/issues).\n\n## Code of Conduct\n\nPlease note that the GeneTonic project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n## License\n\nMIT \u0026copy; Federico Marini\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffedericomarini%2Fgenetonic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffedericomarini%2Fgenetonic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffedericomarini%2Fgenetonic/lists"}