A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
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README.md

BioInstaller

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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

# 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)

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