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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

1.7.5

License

GPL (>= 3)

Maintainer

Sylvain Mareschal

Last Published

August 18th, 2023

Functions in Rgb (1.7.5)

tk.utils

Tk interface utilities
tk.convert

RDT file conversion
tk.browse

R Genome browser
sliceable-class

Class "sliceable"
segOverlap

Merges overlapping segments
singlePlot

Whole genome plot of a drawable list
read.gtf

Parses a GTF2 file
drawable.list

Drawable list constructor
segMerge

Merges consecutive segments
findDrawables

Find drawable objects in memory
RDT storage files

Single refTable object storage
track.genes-class

Class "track.genes"
track-constructors

Track constructors
track.fasta-constructors

Track constructors for FASTA files
tk.tracks

Track management for Genome browser
yline

Compute Y line to avoid collision
track.table-class

Class "track.table"
track.exons-class

Class "track.exons"
track.fasta-class

Class "track.fasta"
track.bam-class

Class "track.bam"
track.bands-class

Class "track.bands"
track.CNV-class

Class "track.CNV"
draw.density

Two-dimensional density plot of a track
draw.seq

Plot a sequence of nucleotides
draw.hist

Histogram plot of a track
draw.bg

Background for track plots
draw.boxes

Boxes plot of a track
draw.points

Scatter plot of a track
Annotation

Annotation track constructors
draw.pileup

Pileup plot of a BAM track
crossable-class

Class "crossable"
draw.steps

Stairway plot of a track
drawable-class

Class "drawable"
hsBands

Homo sapiens GRCh37 chromosome banding
drawable.list-class

Class "drawable.list"
subtrack

Extract elements within a genomic window
refTable-constructor

refTable class constructor
refTable-class

Class "refTable"
hsGenes

Subset of Homo sapiens GRCh37 genes