{"id":22505008,"url":"https://github.com/bcbi/bcbi_base.jl","last_synced_at":"2026-03-19T23:02:26.493Z","repository":{"id":100218823,"uuid":"90858395","full_name":"bcbi/BCBI_base.jl","owner":"bcbi","description":"Julia packages commonly used by the Brown Center for Biomedical Informatics (BCBI)","archived":false,"fork":false,"pushed_at":"2020-02-08T20:32:35.000Z","size":54,"stargazers_count":1,"open_issues_count":4,"forks_count":0,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-03-27T23:23:41.273Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Julia","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/bcbi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":"CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-05-10T11:49:31.000Z","updated_at":"2023-10-29T06:04:16.000Z","dependencies_parsed_at":"2023-04-15T17:19:49.527Z","dependency_job_id":null,"html_url":"https://github.com/bcbi/BCBI_base.jl","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/bcbi/BCBI_base.jl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcbi%2FBCBI_base.jl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcbi%2FBCBI_base.jl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcbi%2FBCBI_base.jl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcbi%2FBCBI_base.jl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bcbi","download_url":"https://codeload.github.com/bcbi/BCBI_base.jl/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcbi%2FBCBI_base.jl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28235811,"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","status":"online","status_checked_at":"2026-01-07T02:00:05.975Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-12-07T00:12:58.470Z","updated_at":"2026-01-07T14:05:29.304Z","avatar_url":"https://github.com/bcbi.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BCBI Metapackage\n\n| Travis CI | Coverage | License |\n|-----------|----------|---------|\n|[![Build Status](https://travis-ci.org/bcbi/BCBI_base.jl.svg?branch=master)](https://travis-ci.org/bcbi/BCBI_base.jl)|[![codecov.io](http://codecov.io/github/bcbi/BCBI_base.jl/coverage.svg?branch=master)](http://codecov.io/githubbcbi/BCBI_base.jl?branch=master)|[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/bcbi/BCBI_base.jl/bcbi_v0.0.0/LICENSE.md)|\n\nThis package is a collection of Julia packages used by the Brown Center for Biomedical Informatics (BCBI). The package serves as a mechanism for installing the various Julia packages most frequently used at BCBI.\n\n\n## Installation\n\n```julia\nPkg.clone(\"https://github.com/bcbi/BCBI_base.jl.git\")\n```\n\n## URSA/STRONGHOLD\n\nSee [instructions](https://github.com/bcbi/BCBI_base.jl/blob/master/STRONGHOLD.md)\n\n## General Usage\n\n* Import package\n\n    ```julia\n    using BCBI_base\n    ```\n\n* Install all packages\n\n    One set at a time\n    ```julia\n    BCBI_base.add(BCBI_base.base_pkgs)\n    BCBI_base.add(BCBI_base.plotting_pkgs)\n    BCBI_base.add(BCBI_base.datasets_pkg)\n    BCBI_base.add(BCBI_base.external_pkgs)\n    BCBI_base.clone(BCBI_base.clone_pkgs)\n    BCBI_base.checkout(BCBI_base.checkout_pkgs)\n    ```\n\n    Alternatively, if you are confident things won't fail\n    ```julia\n    install_all()\n    ````\n\n* Check that installed packages precompile correctly\n\n    It is best to call this from a new/fresh julia session\n\n    ```julia\n    using_all()\n    ```\n\n* Remove packages that are not working (recommended)\n\n    ```julia\n    BCBI_base.clean_up()\n    ```\n\n* Get list of missing \"desired\" packages\n\n    ```julia\n    check_installed()\n    ```\n\n## List of packages\n\n| Base | Plotting | DataSets | R/Python | Cloned\n|------------|--------------|---------------------|---------------------|---------------------|\n|MySQL|PGFPlotsX|RDataSets|RCall|ARules=\u003ehttps://github.com/bcbi/ARules.jl|\n|BioServices|PlotlyJS|VegaDatasets|PyCall|ScikitLearn=\u003ehttps://github.com/cstjean/ScikitLearn.jl.git|\n|ClassImbalance|||Pandas|Gadfly=\u003ehttps://github.com/GiovineItalia/Gadfly.jl.git|\n|Clustering|||Pandas|BioMedQuery=\u003ehttps://github.com/bcbi/BioMedQuery.jl.git|\n|Compat|||Seaborn|Lasso=\u003ehttps://github.com/simonster/Lasso.jl.git|\n|CSV||||PredictMD=\u003ehttps://github.com/bcbi/PredictMD.jl|\n|DataFrames|||||\n|DecisionTree|||||\n|EzXML|||||\n|GLM|||||\n|GLMNet|||||\n|HTTP|||||\n|HypothesisTests|||||\n|IJulia|||||\n|JLD|||||\n|JLD2|||||\n|JuliaDB|||||\n|Lasso|||||\n|LIBSVM|||||\n|LightXML|||||\n|MixedModels|||||\n|Revise|||||\n|ROCAnalysis|||||\n|StatsBase|||||\n|Query|||||\n\n\n* To print the list of packages installed by this version:\n\n\n    ```julia\n    using BCBI_base\n    println(BCBI_base.base_pkgs)\n    println(BCBI_base.plotting_pkgs)\n    println(BCBI_base.external_pkgs)\n    println(BCBI_base.datasets_pkgs)\n    println(BCBI_base.clone_pkgs)\n    println(BCBI_base.checkout_pkgs)\n    ```\n\n\n## Other Dependencies\n\n* The MySQL.jl package depends on a working MySQL installation; instructions can be obtained [here](https://dev.mysql.com/doc/refman/5.7/en/installing.html). For simplicity, macOS users may prefer to install MySQL using [Homebrew](https://brew.sh/).\n\n* The RCall.jl package depends on a working installation of R, which can be obtained [here](https://www.r-project.org/). MacOS users may opt to use [Homebrew](https://brew.sh/) for ease of installation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcbi%2Fbcbi_base.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbcbi%2Fbcbi_base.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcbi%2Fbcbi_base.jl/lists"}