Details

Autor(en) / Beteiligte

• Oróstica, Karen Y
• Verdugo, Ricardo A

Titel

chromPlot: visualization of genomic data in chromosomal context

Ist Teil von

• Bioinformatics (Oxford, England), 2016-08, Vol.32 (15), p.2366-2368

Ort / Verlag

England

Erscheinungsjahr

2016

Quelle

MEDLINE

Beschreibungen/Notizen

• : Visualizing genomic data in chromosomal context can help detecting errors in data processing and may suggest new hypotheses to be tested. Here, we report a new tool for displaying large and diverse genomic data along chromosomes. The software is implemented in R so that visualization can be easily integrated with its numerous packages for processing genomic data. It supports simultaneous visualization of multiple tracks of data. Large genomic regions such as QTLs or synteny tracts may be shown along histograms of number of genes, genetic variants, or any other type of genomic element. Tracks can also contain values for continuous or categorical variables and the user can choose among points, connected lines, colored segments, or histograms for representing data. chromPlot takes data from tables in data.frame in GRanges formats. The information necessary to draw chromosomes for mouse and human is included with the package. For other organisms, chromPlot can read Gap and cytoBandIdeo tables from the UCSC Genome Browser. We present common use cases here, and a full tutorial is included as the package's vignette. chromPlot is distributed under a GLP2 licence at http://www.bioconductor.org raverdugo@u.uchile.cl Supplementary data are available at Bioinformatics online.