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.
- 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
- System monitor
- Task submitting system
- Parallel tasks
- 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
#You can install this package directly from CRAN by running (from within R): install.packages('BioInstaller')
# install.packages("devtools") devtools::install_github("JhuangLab/BioInstaller")
Shiny UI overview
# Start the standalone Shiny application BioInstaller::web(auto_create = TRUE)
- GitHub resource
- GitHub resource meta information
- Non GitHub resource
- Non Github resource meta infrmation
- Web Service
- 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 ...
- GATK, Mutect, VarScan2, FreeBayes, LoFreq, TVC, SomaticSniper, Pindel, Delly, BreakDancer, FusionCatcher, Genome STRiP, CNVnator, CNVkit, SpeedSeq ...
- ANNOVAR, SnpEff, VEP, oncotator ...
- htslib, samtools, bcftools, bedtools, bamtools, vcftools, sratools, picard, HTSeq, seqtk, UCSC Utils(blat, liftOver), bamUtil, jvarkit, bcl2fastq2, fastq_tools ...
- hisat2_reffa, ucsc_reffa, ensemble_reffa ...
- sparsehash, SQLite, pigz, lzo, lzop, bzip2, zlib, armadillo, pxz, ROOT, curl, xz, pcre, R, gatk_bundle, ImageJ, igraph ...
- 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 ...
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
- 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.
Related Other Resources