BioInstaller

Introduction

Accessing and management of various bioinformatics tool/script and database are essential for almost all bioinformatics analysis projects.

There is an urgent need for the development of new all-in-one tools that allows users to search, download, install and share these bioinformatics tool/script and database.

Conda and Spack have done a lot of work and we can use them to conveniently install some bioinformatics software. But there are still many problems with these package managers, such as incompatible to some precompiled programs, little support for the database and other non-software files.

BioInstaller is a comprehensive R package to integrate bioinformatics resources, such as software/script and database. It provides the R, Shiny web application, and the GitHub forum. Hundreds of bioinformatics tool/script and database have been included in BioInstaller.

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

sebymusundi/BioInstaller