karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
By Bernat Gel, Eduard Serra. bioRxiv, 2017
661 citations recorded by the source corpus.
Motivation Data visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species. Results We have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation. Availability karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR) Contact bgel@igtp.cat
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/02f440f61146df081b387fa339a7adf30e2e4886
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Citations in the corpus
- NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, methodology): “SDs hotspots calculation and visualization were carried out with R packages: tidyverse [51], rtracklayer [52], plyranges [53], and karyoploteR [54].”
- The complete sequence of a human genome (2021, methodology): “SD density in 10 kbp windows was computed using the kpPlotDensity (111) function and colored by log of the window density.”