{"id":14068946,"url":"https://github.com/JhuangLab/BioInstaller","last_synced_at":"2025-07-30T05:30:48.414Z","repository":{"id":84536465,"uuid":"85032167","full_name":"JhuangLab/BioInstaller","owner":"JhuangLab","description":"A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform","archived":false,"fork":false,"pushed_at":"2023-01-08T23:47:19.000Z","size":3059,"stargazers_count":56,"open_issues_count":12,"forks_count":13,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-10-30T21:03:03.170Z","etag":null,"topics":["bioinformatics-analysis","installer","installer-script","ngs-analysis"],"latest_commit_sha":null,"homepage":"","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/JhuangLab.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-03-15T05:20:19.000Z","updated_at":"2024-01-06T04:29:52.000Z","dependencies_parsed_at":"2023-10-20T20:44:32.765Z","dependency_job_id":null,"html_url":"https://github.com/JhuangLab/BioInstaller","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JhuangLab%2FBioInstaller","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JhuangLab%2FBioInstaller/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JhuangLab%2FBioInstaller/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JhuangLab%2FBioInstaller/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JhuangLab","download_url":"https://codeload.github.com/JhuangLab/BioInstaller/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228092056,"owners_count":17868122,"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":["bioinformatics-analysis","installer","installer-script","ngs-analysis"],"created_at":"2024-08-13T07:06:30.062Z","updated_at":"2024-12-04T10:30:37.020Z","avatar_url":"https://github.com/JhuangLab.png","language":"R","readme":"# BioInstaller \u003cimg src=\"https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/man/figures/logo.png\" align=\"right\" /\u003e\n\n[![Build\nStatus](https://img.shields.io/circleci/project/github/JhuangLab/BioInstaller/master.svg)](https://circleci.com/gh/JhuangLab/BioInstaller/tree/master)\n[![CRAN](http://www.r-pkg.org/badges/version/BioInstaller)](https://cran.r-project.org/package=BioInstaller)\n[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.1343914.svg)](https://zenodo.org/record/1343914)\n[![Downloads](http://cranlogs.r-pkg.org/badges/BioInstaller?color=brightgreen)](http://www.r-pkg.org/pkg/BioInstaller)\n[![codecov](https://codecov.io/github/JhuangLab/BioInstaller/branch/master/graphs/badge.svg)](https://codecov.io/github/JhuangLab/BioInstaller)\n\n## Introduction\n\nThe increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. \n\nR language, as the most popular programming language for statistics, biological data analysis, and big data, has enabled diverse and free R packages (\u003e14000) for different types of applications. However, due to the lack of high-performance and open-source cloud platforms based on R (e.g., Galaxy for Python users), it is still difficult for R users, especially those without web development skills, to construct interactive and reproducible biological data analysis applications supporting the upload and management of files, long-time computation, task submission, tracking of output files, exception handling, logging, export of plots and tables, and extendible plugin systems.\n\nThe collection, management, and share of various bioinformatics tools/scripts and databases are also essential for almost all bioinformatics analysis projects.\n\nHere, we established a new platform to construct interactive and reproducible biological data analysis applications based on R language. This platform contains diverse user interfaces, including the R functions and R Shiny application, REST APIs, and support for collecting, managing, sharing, and utilizing massive bioinformatics tools/scripts and databases.\n\n**Feature**:\n\n  - Easy-to-use\n  - User-friendly Shiny application\n  - Integrative platform of Databases and bioinformatics resources\n  - Open source and completely free\n  - One-click to download and install bioinformatics resources (via R, Shiny or Opencpu REST APIs)\n  - More attention for those software and database resource that have not been\n    by other tools\n  - Logging\n  - System monitor\n  - Task submitting system\n  - Parallel tasks\n\n**Field**\n\n  - Quality Control\n  - Alignment And Assembly\n  - Alternative Splicing\n  - ChIP-seq analysis\n  - Gene Expression Data Analysis\n  - Variant Detection\n  - Variant Annotation\n  - Virus Related\n  - Statistical and Visualization\n  - Noncoding RNA Related Database\n  - Cancer Genomics Database\n  - Regulator Related Database\n  - eQTL Related Database\n  - Clinical Annotation\n  - Drugs Database\n  - Proteomic Database\n  - Software Dependence Database \n  - ......\n\n\u003cimg src=\"https://raw.githubusercontent.com/JhuangLab/BioInstaller/develop/man/figures/design_of_bioInstaller.jpg\" align=\"middle\" /\u003e\n\n**Note:** We are developing [bget](https://github.com/openbiox/bget) and [bioshiny](https://github.com/openbiox/bioshiny) projects independently for simplify the functions of download and shiny. \n\n- [bget](https://github.com/openbiox/bget) is an golang-based command-line tool that do not need to install any R packages. \n- [bioshiny](https://github.com/openbiox/bioshiny) is the core shiny application of previous BioInstaller package.\n\n## Installation\n\n### CRAN\n\n``` r\n#You can install this package directly from CRAN by running (from within R):\ninstall.packages('BioInstaller')\n```\n\n### Github\n\n``` bash\n# install.packages(\"devtools\")\ndevtools::install_github(\"JhuangLab/BioInstaller\")\n\n```\n## Shiny application\n\n**Note**, the Shiny application of BioInstaller was migrated to [bioshiny](https://github.com/openbiox/bioshiny) project. All shiny files in this package have been removed for reducing package size.\n\nIn the new project, we are developing more free plugins of bioshiny for various bioinformatics data analysis. \n\n```bash\necho 'export BIO_SOFTWARES_DB_ACTIVE=\"~/.bioshiny/info.yaml\" \u003e\u003e ~/.bashrc'\necho 'export BIOSHINY_CONFIG=\"~/.bioshiny/shiny.config.yaml\" \u003e\u003e ~/.bashrc'\n. ~/.bashrc\n\n# Start the standalone Shiny application\nwget https://raw.githubusercontent.com/openbiox/bioshiny/master/bin/bioshiny_deps_r\nwget https://raw.githubusercontent.com/openbiox/bioshiny/master/bin/bioshiny_start\nchmod a+x bioshiny_deps_r\nchmod a+x bioshiny_start\n./bioshiny_deps_r\n\n# Start Shiny application workers\nRscript -e \"bioshiny::set_shiny_workers(1)\"\n./bioshiny_start\n\n# or use yarn\nyarn global add bioshiny\nbioshiny_deps_r\nRscript -e \"bioshiny::set_shiny_workers(1)\"\nbioshiny_start\n```\n\n[spack](https://spack.io/) and [miniconda](https://docs.conda.io/en/latest/miniconda.html) are required for extra functions.\n\n## Contributed Resources\n\n  - [GitHub\n    resource](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/github/github.toml)\n  - GitHub resource [meta\n    information](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/github/github_meta.toml)\n  - [Non GitHub\n    resource](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/nongithub/nongithub.toml)\n  - Non Github resource [meta\n    infrmation](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/nongithub/nongithub_meta.toml)\n  - [Database](https://github.com/JhuangLab/BioInstaller/tree/master/inst/extdata/config/db)\n  - [Web\n    Service](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/web/web_meta.toml)\n  - [Docker](https://github.com/JhuangLab/BioInstaller/blob/master/inst/extdata/config/docker/docker.toml)\n\n## Support Summary\n\n**Quality Control:**\n\n  - FastQC, PRINSEQ, SolexaQA, FASTX-Toolkit ...\n\n**Alignment and Assembly:**\n\n  - BWA, STAR, TMAP, Bowtie, Bowtie2, tophat2, hisat2, GMAP-GSNAP,\n    ABySS, SSAHA2, Velvet, Edean, Trinity, oases, RUM, MapSplice2,\n    NovoAlign ...\n\n**Variant Detection:**\n\n  - GATK, Mutect, VarScan2, FreeBayes, LoFreq, TVC, SomaticSniper,\n    Pindel, Delly, BreakDancer, FusionCatcher, Genome STRiP, CNVnator,\n    CNVkit, SpeedSeq ...\n\n**Variant Annotation:**\n\n  - ANNOVAR, SnpEff, VEP, oncotator ...\n\n**Utils:**\n\n  - htslib, samtools, bcftools, bedtools, bamtools, vcftools, sratools,\n    picard, HTSeq, seqtk, UCSC Utils(blat, liftOver), bamUtil, jvarkit,\n    bcl2fastq2, fastq\\_tools ...\n\n**Genome:**\n\n  - hisat2\\_reffa, ucsc\\_reffa, ensemble\\_reffa ...\n\n**Others:**\n\n  - sparsehash, SQLite, pigz, lzo, lzop, bzip2, zlib, armadillo, pxz,\n    ROOT, curl, xz, pcre, R, gatk\\_bundle, ImageJ, igraph ...\n\n**Databases:**\n\n  - ANNOVAR, blast, CSCD, GATK\\_Bundle, biosystems, civic, denovo\\_db,\n    dgidb, diseaseenhancer, drugbank, ecodrug, expression\\_atlas,\n    funcoup, gtex, hpo, inbiomap, interpro, medreaders, mndr, msdd,\n    omim, pancanqtl, proteinatlas, remap2, rsnp3, seecancer,\n    srnanalyzer, superdrug2, tumorfusions, varcards ...\n\n## Docker\n\nYou can use the BioInstaller in Docker since v0.3.0. Shiny application was supported since v0.3.5.\n\n``` bash\ndocker pull bioinstaller/bioinstaller\ndocker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller/bioinstaller\n```\n\nService list:\n\n- localhost/ocpu/ Opencpu service\n- localhost/shiny/BioInstaller Shiny service\n- localhost/rstudio/ Rstudio server (opencpu/opencpu)\n\n## Citation\n\n- Li J, Cui B, Dai Y, et al. BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform[J]. PeerJ, 2018, 6:e5853.\n\n## How to contribute?\n\nPlease fork the [GitHub BioInstaller\nrepository](https://github.com/JhuangLab/BioInstaller), modify it, and\nsubmit a pull request to us. Especialy, the files list in `contributed\nsection` should be modified when you see a tool or database that not be\nincluded in the other software warehouse.\n\n## Maintainer\n\n[Jianfeng Li](https://github.com/Miachol)\n\n## License\n\nR package:\n\n[MIT](https://en.wikipedia.org/wiki/MIT_License)\n\nRelated Other Resources\n\nCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License\n","funding_links":[],"categories":["R"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJhuangLab%2FBioInstaller","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FJhuangLab%2FBioInstaller","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJhuangLab%2FBioInstaller/lists"}