/orenogb

Visualization command for genomic data

Primary LanguageRMIT LicenseMIT

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

demo

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

demo

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

demo

Search by Gene Symbol

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

demo

Human Genome

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

demo

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