Package: Rgb 1.7.6

Rgb: The R Genome Browser

Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as genes or transcripts), and an interactive interface to browse them.

Authors:Sylvain Mareschal

Rgb_1.7.6.tar.gz
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Rgb.pdf |Rgb.html✨
Rgb/json (API)
NEWS

# Install 'Rgb' in R:
install.packages('Rgb', repos = c('https://maressyl.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/maressyl/r.rgb/issues

Datasets:
  • hsBands - Homo sapiens GRCh37 chromosome banding
  • hsGenes - Subset of Homo sapiens GRCh37 genes

On CRAN:

43 exports 1 stars 0.84 score 0 dependencies 56 scripts 204 downloads

Last updated 9 months agofrom:4a09ec5156. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-win-x86_64NOTESep 05 2024
R-4.5-linux-x86_64NOTESep 05 2024
R-4.4-win-x86_64NOTESep 05 2024
R-4.4-mac-x86_64NOTESep 05 2024
R-4.4-mac-aarch64NOTESep 05 2024
R-4.3-win-x86_64OKSep 05 2024
R-4.3-mac-x86_64OKSep 05 2024
R-4.3-mac-aarch64OKSep 05 2024

Exports:browsePlotdraw.bgdraw.boxesdraw.densitydraw.histdraw.pileupdraw.pointsdraw.seqdraw.stepsdrawable.listfindDrawableshandleistrackread.gtfreadRDTrefTablesaveRDTsegMergesegOverlapsinglePlotsizetracksubtracktk.browsetk.converttk.filetk.filestk.foldertk.trackstrack.bamtrack.bandstrack.bands.UCSCtrack.CNVtrack.CNV.DGVtrack.exonstrack.exons.CCDStrack.exons.GENCODEtrack.fasta.collectiontrack.fasta.multitrack.genestrack.genes.NCBItrack.tabletrack.table.GTFyline

Dependencies:

How-to guide to Rgb

Rendered fromHowto.Rtexusingutils::Sweaveon Sep 05 2024.

Last update: 2023-08-17
Started: 2015-02-08

Readme and manuals

Help Manual

Help pageTopics
Annotation track constructorsAnnotation track.bands.UCSC track.CNV.DGV track.exons.CCDS track.exons.GENCODE track.genes.NCBI track.table.GTF
Class '"crossable"'crossable-class
Background for track plotsdraw.bg
Boxes plot of a trackdraw.boxes
Two-dimensional density plot of a trackdraw.density
Histogram plot of a trackdraw.hist
Pileup plot of a BAM trackdraw.pileup
Scatter plot of a trackdraw.points
Plot a sequence of nucleotidesdraw.seq
Stairway plot of a trackdraw.steps
Class '"drawable"'drawable-class
Drawable list constructordrawable.list
Class '"drawable.list"'drawable.list-class
Find drawable objects in memoryfindDrawables
Homo sapiens GRCh37 chromosome bandinghsBands
Subset of Homo sapiens GRCh37 geneshsGenes
Single refTable object storagereadRDT saveRDT
Parses a GTF2 fileread.gtf
Class '"refTable"'refTable-class
refTable class constructorrefTable
Merges consecutive segmentssegMerge
Merges overlapping segmentssegOverlap
Whole genome plot of a drawable listsinglePlot
Class '"sliceable"'sliceable-class
Extract elements within a genomic windowistrack sizetrack subtrack
R Genome browserbrowsePlot tk.browse
RDT file conversiontk.convert
Track management for Genome browsertk.tracks
Tk interface utilitieshandle tk.file tk.files tk.folder
Track constructorstrack-constructors track.bam track.bands track.CNV track.exons track.genes track.table
Class '"track.bam"'track.bam-class
Class '"track.bands"'track.bands-class
Class '"track.CNV"'track.CNV-class
Class '"track.exons"'track.exons-class
Class '"track.fasta"'track.fasta-class
Track constructors for FASTA filestrack.fasta-constructors track.fasta.collection track.fasta.multi
Class '"track.genes"'track.genes-class
Class '"track.table"'track.table-class
Compute Y line to avoid collisionyline