Integrator of Bioinformatics Resources

Can be used to integrate massive bioinformatics resources, such as tool/script and database. It provides the R functions and Shiny web application. Hundreds of bioinformatics tool/script and database have been included.


BuildStatus CRAN Zenodo Downloads codecov

Introduction

The 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.

R language, as the most popular programming language for statistics, biological data analysis, and big data, has enabled diverse and free R packages (>14000) 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.

The collection, management, and share of various bioinformatics tools/scripts and databases are also essential for almost all bioinformatics analysis projects.

Here, 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.

Feature:

  • Easy-to-use
  • User-friendly Shiny application
  • Integrative platform of Databases and bioinformatics resources
  • Open source and completely free
  • One-click to download and install bioinformatics resources (via R, Shiny or Opencpu REST APIs)
  • More attention for those software and database resource that have not been by other tools
  • Logging
  • System monitor
  • Task submitting system
  • Parallel tasks

Field

  • Quality Control
  • Alignment And Assembly
  • Alternative Splicing
  • ChIP-seq analysis
  • Gene Expression Data Analysis
  • Variant Detection
  • Variant Annotation
  • Virus Related
  • Statistical and Visualization
  • Noncoding RNA Related Database
  • Cancer Genomics Database
  • Regulator Related Database
  • eQTL Related Database
  • Clinical Annotation
  • Drugs Database
  • Proteomic Database
  • Software Dependence Database
  • ......

Installation

CRAN

#You can install this package directly from CRAN by running (from within R):
install.packages('BioInstaller')

Github

# install.packages("devtools")
devtools::install_github("JhuangLab/BioInstaller")
 

Shiny UI overview

Note, the Shiny application of BioInstaller was migrated to bioshiny project. All shiny files in this package will deprecated soon.

In the new project, we will provides one-click method (command line and Shiny UI) to create bioshiny application and its plugins. We are also developing more free plugins of bioshiny for various bioinformatics data analysis.

# Start the standalone Shiny application
BioInstaller::web(auto_create = TRUE)

Contributed Resources

Support Summary

Quality Control:

  • FastQC, PRINSEQ, SolexaQA, FASTX-Toolkit ...

Alignment and Assembly:

  • BWA, STAR, TMAP, Bowtie, Bowtie2, tophat2, hisat2, GMAP-GSNAP, ABySS, SSAHA2, Velvet, Edean, Trinity, oases, RUM, MapSplice2, NovoAlign ...

Variant Detection:

  • GATK, Mutect, VarScan2, FreeBayes, LoFreq, TVC, SomaticSniper, Pindel, Delly, BreakDancer, FusionCatcher, Genome STRiP, CNVnator, CNVkit, SpeedSeq ...

Variant Annotation:

  • ANNOVAR, SnpEff, VEP, oncotator ...

Utils:

  • htslib, samtools, bcftools, bedtools, bamtools, vcftools, sratools, picard, HTSeq, seqtk, UCSC Utils(blat, liftOver), bamUtil, jvarkit, bcl2fastq2, fastq_tools ...

Genome:

  • hisat2_reffa, ucsc_reffa, ensemble_reffa ...

Others:

  • sparsehash, SQLite, pigz, lzo, lzop, bzip2, zlib, armadillo, pxz, ROOT, curl, xz, pcre, R, gatk_bundle, ImageJ, igraph ...

Databases:

  • ANNOVAR, blast, CSCD, GATK_Bundle, biosystems, civic, denovo_db, dgidb, diseaseenhancer, drugbank, ecodrug, expression_atlas, funcoup, gtex, hpo, inbiomap, interpro, medreaders, mndr, msdd, omim, pancanqtl, proteinatlas, remap2, rsnp3, seecancer, srnanalyzer, superdrug2, tumorfusions, varcards ...

Docker

You can use the BioInstaller in Docker since v0.3.0. Shiny application was supported since v0.3.5.

docker pull bioinstaller/bioinstaller
docker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller/bioinstaller

Service list:

  • localhost/ocpu/ Opencpu service
  • localhost/shiny/BioInstaller Shiny service
  • localhost/rstudio/ Rstudio server (opencpu/opencpu)

Citation

  • 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.

How to contribute?

Please fork the GitHub BioInstaller repository, modify it, and submit a pull request to us. Especialy, the files list in contributed section should be modified when you see a tool or database that not be included in the other software warehouse.

Maintainer

Jianfeng Li

License

R package:

MIT

Related Other Resources

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License

News

BioInstaller 0.3.7

New features

  • support bitbucket repo
  • remove function "check_shiny_dep" use pacman install dependences
  • add new databases and tools (meta and files)

Minor bugs fixed

  • fix "version_avaliable" to "version_available" in ~10 item

BioInstaller 0.3.6

New features

  • add copy_plugins and copy_configs functions to restore the plugins and config
  • use fromJSON to access the github APIs, which can avoid the SSL problem on windows platform

BioInstaller 0.3.5.7000

Minor bugs fixed

  • Add conda and spack in the Docker image

BioInstaller 0.3.5.6000

New features

  • Shiny application supported

  • Numbers increased of included items, especialy the databases

  • Use github forum

  • Add parameter overwrite in install.bioinfo

  • Add Opencpu, Shiny and Rstudio service in Docker container

  • Use 'Setting' module in Shiny application to manage the variables

Minor bugs fixed

  • Check and confirm delete the existing dir only when clone a github project

BioInstaller 0.3.3

New features

  • Multiple resources file be supported

  • Adjust and set db, github, nongithub, web and docker in inst/extdata/config

  • Meta information of software and database be added in newly supported items

  • Decompress can be auto-recognized

  • Docker supported

Minor bugs fixed

  • change.info default is to write tempfile() now

  • Fixed a bug when set save.to.db to FALSE. It can raise installed fail

BioInstaller 0.2.1

New features

  • ANNOVAR databases can be download using inst/extdata/databases/ANNOVAR.toml

  • Move databases toml file to inst/extdata/databases/

  • local.source be supported (Don't need download the source code again when it were download already)

  • Function docker.pull and docker.search be added to download and search docker repo

  • Function craw.all.versions be added to crawl source code of all version (Sotwares or databases)

BioInstaller 0.1.2

New features

  • #R# CMD #R# marked the R CMD need to be runed

  • glue parse be supported

  • Softwares versions of github.cfg be fetched from github API

  • destdir and download.dir can be setted respectively

  • verbose default is TRUE, show log infomation

Minor bugs fixed

  • Fix unlink() clean tests files fail on windows (force = TRUE)

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BioInstaller")

0.3.7 by Jianfeng Li, 10 months ago


https://github.com/JhuangLab/BioInstaller


Report a bug at https://github.com/JhuangLab/BioInstaller/issues


Browse source code at https://github.com/cran/BioInstaller


Authors: Jianfeng Li [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports stringr, futile.logger, configr, jsonlite, git2r, R.utils, RCurl, rvest, devtools, stringi, shiny, liteq

Suggests knitr, rmarkdown, testthat, prettydoc, DT


See at CRAN