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R genome browser

R package to efficiently browse and handle genomic data.

Availability

A short presentation of the project can be found on my personnal website.

Release sources and builds can be found in the CRAN repository :

Development sources are freely available on GitHub :

All this material is freely distributed under the GNU Public License 3, shipped with sources and builds.

Support

Bugs, suggestions and help requests should be submitted using GitHub's Issues (see 'Availability').

Changelog

Release updates are tracked by the NEWS.Rd file, browsable on the CRAN repository (see 'Availability').

Individual commits can be followed on GitHub (see 'Availability').

Credits

Sylvain Mareschal <maressyl@gmail.com>

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Version

Install

install.packages('Rgb')

Monthly Downloads

40

Version

1.6.1

License

GPL (>= 3)

Maintainer

Sylvain Mareschal

Last Published

March 18th, 2018

Functions in Rgb (1.6.1)

draw.bg

Background for track plots
draw.pileup

Pileup plot of a BAM track
Annotation

Annotation track constructors
draw.boxes

Boxes plot of a track
draw.steps

Stairway plot of a track
crossable-class

Class "crossable"
refTable-class

Class "refTable"
drawable-class

Class "drawable"
findDrawables

Find drawable objects in memory
draw.hist

Histogram plot of a track
segMerge

Merges consecutive segments
hsFeatures

Homo sapiens GRCh37 genomic features
draw.points

Scatter plot of a track
tk.browse

R Genome browser
sliceable-class

Class "sliceable"
read.gtf

Parses a GTF2 file
draw.seq

Plot a sequence of nucleotides
track-constructors

Track constructors
track.CNV-class

Class "track.CNV"
drawable.list-class

Class "drawable.list"
subtrack

Extract elements within a genomic window
tk.tracks

Track management for Genome browser
track.bam-class

Class "track.bam"
tk.utils

Tk interface utilities
RDT storage files

Single refTable object storage
track.genes-class

Class "track.genes"
track.fasta-class

Class "track.fasta"
refTable-constructor

refTable class constructor
track.bands-class

Class "track.bands"
yline

Compute Y line to avoid collision
drawable.list

Drawable list constructor
track.exons-class

Class "track.exons"
tk.convert

RDT file conversion
track.table-class

Class "track.table"
segOverlap

Merges overlapping segments
singlePlot

Whole genome plot of a drawable list
track.fasta-constructors

Track constructors for FASTA files