karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data.
Bernat Gel,Eduard Serra +1 more
TLDR
KaryoploteR as mentioned in this paper is an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them, which allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.Abstract:
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 and implementation karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR) and at the examples and tutorial page at https://bernatgel.github.io/karyoploter_tutorial. Contact bgel@igtp.cat.read more
Citations
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Journal ArticleDOI
The complete sequence of a human genome
Sergey Koren,Sergey Nurk,Mikko Rautiainen,B Ren,Weijun Zhu,Richard Lawless,Саидмуродов Мамур Таирович +6 more
TL;DR: The T2T-CHM13-T2T Consortium presented a complete 3.055 billion-base pair sequence of a human genome, including gapless assemblies for all chromosomes except Y, corrected errors in the prior references, and introduced nearly 200 million base pairs of sequence containing gene predictions, 99 of which are predicted to be protein coding as discussed by the authors .
Journal ArticleDOI
Characterizing the Major Structural Variant Alleles of the Human Genome
Peter A. Audano,Arvis Sulovari,Tina A. Graves-Lindsay,Stuart Cantsilieris,Melanie Sorensen,AnneMarie E. Welch,Max L. Dougherty,Bradley J. Nelson,Ankeeta Shah,Susan K. Dutcher,Wesley C. Warren,Vincent Magrini,Vincent Magrini,Sean McGrath,Yang I. Li,Richard K. Wilson,Richard K. Wilson,Evan E. Eichler +17 more
TL;DR: A ninefold SV bias toward the last 5 Mbp of human chromosomes is reported with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome.
Journal ArticleDOI
Genomic architecture and introgression shape a butterfly radiation
Nathaniel B. Edelman,Paul B. Frandsen,Paul B. Frandsen,Michael Miyagi,Bernardo J. Clavijo,John W. Davey,John W. Davey,Rebecca B. Dikow,Gonzalo García-Accinelli,Steven M. Van Belleghem,Nick Patterson,Nick Patterson,Daniel E. Neafsey,Daniel E. Neafsey,Richard Challis,Sujai Kumar,Gilson R. P. Moreira,Camilo Salazar,Mathieu Chouteau,Brian A. Counterman,Riccardo Papa,Riccardo Papa,Mark Blaxter,Robert D. Reed,Kanchon K. Dasmahapatra,Marcus R. Kronforst,Mathieu Joron,Chris D. Jiggins,W. Owen McMillan,Federica Di Palma,Andrew J. Blumberg,John Wakeley,David B. Jaffe,James Mallet +33 more
TL;DR: Tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome, and a hitherto unknown inversion that traps a color pattern switch locus is identified.
Journal ArticleDOI
The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies.
Lindsay Angus,Marcel Smid,Saskia M Wilting,Job van Riet,Arne Van Hoeck,Luan Nguyen,Serena Nik-Zainal,Tessa G Steenbruggen,Vivianne C. G. Tjan-Heijnen,Mariette Labots,Johanna M. G. H. van Riel,Haiko J. Bloemendal,Neeltje Steeghs,Martijn P. Lolkema,Emile E. Voest,Harmen J.G. van de Werken,Agnes Jager,Edwin Cuppen,Stefan Sleijfer,John W.M. Martens +19 more
TL;DR: Whole-genome sequencing of metastatic biopsies from 442 patients with breast cancer provides insights into metastatic disease, including associations of genomic features with prior treatments and identification of therapeutic vulnerabilities.
Journal ArticleDOI
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms.
Zhaodong Hao,Zhaodong Hao,Dekang Lv,Ying Ge,Jisen Shi,Dolf Weijers,Guangchuang Yu,Jinhui Chen +7 more
TL;DR: The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.
References
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Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Book ChapterDOI
Visualizing Genomic Data Using Gviz and Bioconductor.
Florian Hahne,Robert Ivanek +1 more
TL;DR: The Gviz package offers a flexible framework to visualize genomic data in the context of a variety of different genome annotation features, and greatly facilitates the production of publication-ready figures of genomic loci.
Journal ArticleDOI
RCircos: an R package for Circos 2D track plots
TL;DR: RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data.
Journal ArticleDOI
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests
Bernat Gel,Anna Díez-Villanueva,Eduard Serra,Marcus Buschbeck,Miguel A. Peinado,Roberto Malinverni +5 more
TL;DR: regioneR as discussed by the authors is an R package that implements a permutation test framework specifically designed to work with genomic regions, which is fully customizable allowing the use of custom strategies to adapt it to specific questions.
Journal ArticleDOI
ggbio: an R package for extending the grammar of graphics for genomic data.
TL;DR: Ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data, is introduced, which provides detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overview through karyogram, circular and grand linear layouts.
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