{"id":38520300,"url":"https://github.com/gosling-lang/grosling","last_synced_at":"2026-01-17T06:38:59.154Z","repository":{"id":48327038,"uuid":"516544076","full_name":"gosling-lang/grosling","owner":"gosling-lang","description":"R interface to 'Gos'","archived":false,"fork":false,"pushed_at":"2023-02-23T14:38:49.000Z","size":58,"stargazers_count":39,"open_issues_count":3,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-12-03T13:30:57.096Z","etag":null,"topics":["hidivelab"],"latest_commit_sha":null,"homepage":"https://gosling-lang.github.io/grosling","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gosling-lang.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-07-21T22:58:29.000Z","updated_at":"2025-06-24T15:15:32.000Z","dependencies_parsed_at":"2022-09-15T16:20:16.251Z","dependency_job_id":null,"html_url":"https://github.com/gosling-lang/grosling","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/gosling-lang/grosling","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gosling-lang%2Fgrosling","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gosling-lang%2Fgrosling/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gosling-lang%2Fgrosling/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gosling-lang%2Fgrosling/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gosling-lang","download_url":"https://codeload.github.com/gosling-lang/grosling/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gosling-lang%2Fgrosling/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28502704,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T04:31:57.058Z","status":"ssl_error","status_checked_at":"2026-01-17T04:31:45.816Z","response_time":85,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["hidivelab"],"created_at":"2026-01-17T06:38:58.533Z","updated_at":"2026-01-17T06:38:59.149Z","avatar_url":"https://github.com/gosling-lang.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(collapse = TRUE)\n```\n\n**Here be dragons** 🐉\n\n# g(r)osling\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThe goal of **g(r)osling** is to help you build interactive genomics visualizations with \n[Gosling](https://github.com/gosling-lang/gosling.js). This package uses \n[reticulate](https://rstudio.github.io/reticulate/) to provide an interface\nto the [Gos](https://github.com/gosling-lang/gos) Python package.\n\n\n## Example\n\n```{r, eval = FALSE}\nlibrary(gosling)\n\ndata \u003c- gos$bigwig(\n  url = \"https://s3.amazonaws.com/gosling-lang.org/data/ExcitatoryNeurons-insertions_bin100_RIPnorm.bw\",\n  column = \"position\",\n  value = \"peak\"\n)\n\ntrack \u003c- gos$Track(data, height = 100)$mark_point()$encode(\n  x = gos$X(\"position:G\"),\n  y = gos$Y(\"peak:Q\")\n)\n\ntrack$view()\n```\n\n![Gosling visualization](https://user-images.githubusercontent.com/24403730/180341226-a9ac36b4-47cb-40d8-bfd2-a2e6f18c153f.png)\n\n## Installation\n\nYou can install the development version of gosling like so:\n\n``` r\ndevtools::install_github(\"gosling-lang/grosling\") \n```\n\nBecause of Python, there may be some additional installation steps.\n\n1.) Python must be installed on your system. We recommend `conda`.\n\n2.) Create a conda environment called `\"r-reticulate\"`. It is [recommended](https://rstudio.github.io/reticulate/articles/python_packages.html) \nto use this environment name for all packages that use reticulate. \n\n3.) Install Gos into your `\"r-reticulate\"` environment using `gosling::install_gosling()`.\n\nYou may wish to add a line like this to the `.First()` function in your `.Rprofile`:\n\n```r\nreticulate::use_condaenv(\"r-reticulate\")\n```\n\nThe `use_condaenv()` function is called to provide a hint to reticulate on which Python environment to use.\n\n\n## Local Data\n\nGos [transparently serves](https://gosling-lang.github.io/gos/user_guide/local_data.html) \nlocal and in-memory datasets for the Gosling client via a background data server. \nThis feature is enabled automatically whenever a local file path is \ndetected (rather than a URL).\n\nDue to [a temporary limitation with `reticulate`](https://github.com/rstudio/reticulate/issues/515#issuecomment-1196609327),\nsome additional setup is required to enable this feature in **grosling**. Hopefully\nthis will be resolved in `reticulate` soon, but the current workaround is shown below.\n\n```{r load_loop, eval = FALSE}\nlibrary(gosling)\n\n### Setup reticulate to continually yield R \u003c\u003e Python. You only need to run this *once*.\nlocal({\n  reticulate::py_run_string(\"from time import sleep\")\n  py_yield_and_register_next_yield \u003c- function() {\n    reticulate::py_eval(\"sleep(0.001)\")\n    later::later(py_yield_and_register_next_yield, .001)\n    invisible()\n  }\n  later::later(py_yield_and_register_next_yield)\n})\n###\n\nfile \u003c- \"./ExcitatoryNeurons-insertions_bin100_RIPnorm.bw\" # local file\ndata \u003c- gos$bigwig(file, column = \"position\", value = \"peak\")\n\ntrack \u003c- gos$Track(data, height = 100, width = 750)$mark_bar()$encode(\n  x = gos$X(\"position:G\"),\n  y = gos$Y(\"peak:Q\"),\n  color = gos$Color(\"peak:Q\")\n)\n\ntrack$view()\n```\n\n![Gosling visualization using local file](https://user-images.githubusercontent.com/24403730/181269342-9e8d1246-d227-4850-b1ae-66f747654369.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgosling-lang%2Fgrosling","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgosling-lang%2Fgrosling","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgosling-lang%2Fgrosling/lists"}