Orenogb

Visualization command for genomic data

Description

• just type simple command on your terminal
• beautiful visualization by ggbio and ggplot2
• semantic zoom
• eaily loading of transcriptome annotation
• search by gene Symbol
• choose species

Demo

$ R --slave --vanilla -f orenogb.R --args coordination mm10 chr17 35400000 35600000 1 Quartz_01.bam,Quartz_02.bam demo/demo.pdf

Exponential notation

$ R --slave --vanilla -f orenogb.R --args coordination mm10 chr17 3.55e7+2880 3.55e7+16079 1 Quartz_01.bam,Quartz_02.bam demo/demo2.pdf

Semantic Zoom

$ R --slave --vanilla -f orenogb.R --args coordination mm10 chr17 35502880 35516079 1/200 Quartz_01.bam,Quartz_02.bam demo/demo3.pdf

Search by Gene Symbol

$ R --slave --vanilla -f orenogb.R --args gene mm10 Pou5f1 1 Quartz_01.bam,Quartz_02.bam demo/demo4.pdf

Human Genome

$ R --slave --vanilla -f orenogb.R --args gene hg19 POU5F1 1 Smart-Seq2_01.bam,Smart-Seq2_02.bam demo/demo5.pdf

Requirement

• R
• Bioconductor Software Packages
  • ggbio
  • GenomicRanges
  • GenomicAlignments
• Bioconductor Annotation Packages
  • Mus.musculus, Homo.sapiens, ...
  • BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, ...

Usage

$ R --slave --vanilla -f orenogb.R --args [mode] [genome] [chr] [start bp] [end bp] [zoom] [bam1,bam2,...] [output file]

Install

$ git clone git@github.com:dritoshi/orenogb.git
$ cd orenogb
$ sudo R
R> source("http://bioconductor.org/biocLite.R")
R> biocLite(c("ggbio", "GenomicRanges", "GenomicAlignments")
R> biocLite(c("Mus.musculus", "BSgenome.Mmusculus.UCSC.mm10"))
R> biocLite(c("Homo.sapiens", "BSgenome.Hsapiens.UCSC.hg19"))    

ToDo

• choose species
• wapper by shell script
• unit test
• deamonaize R script
• draw sample name

Contribution

Licence

MIT

Author

dritoshi