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Merge pull request #4941 from galaxyproject/mermaid-pierce
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Cite circos tool
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shiltemann committed May 15, 2024
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84 changes: 48 additions & 36 deletions topics/visualisation/tutorials/circos/tutorial.bib
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@article{krzywinski2009circos,
title={Circos: an information aesthetic for comparative genomics},
author={Krzywinski, Martin and Schein, Jacqueline and Birol, Inanc and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A},
journal={Genome research},
volume={19},
number={9},
pages={1639--1645},
year={2009},
publisher={Cold Spring Harbor Lab}
title = {Circos: an information aesthetic for comparative genomics},
author = {Krzywinski, Martin and Schein, Jacqueline and Birol, Inanc and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A},
year = 2009,
journal = {Genome research},
publisher = {Cold Spring Harbor Lab},
volume = 19,
number = 9,
pages = {1639--1645},
}

@article{kosugi2019comprehensive,
title={Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing},
author={Kosugi, Shunichi and Momozawa, Yukihide and Liu, Xiaoxi and Terao, Chikashi and Kubo, Michiaki and Kamatani, Yoichiro},
journal={Genome biology},
volume={20},
number={1},
pages={117},
year={2019},
publisher={BioMed Central}
title = {Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing},
author = {Kosugi, Shunichi and Momozawa, Yukihide and Liu, Xiaoxi and Terao, Chikashi and Kubo, Michiaki and Kamatani, Yoichiro},
year = 2019,
journal = {Genome biology},
publisher = {BioMed Central},
volume = 20,
number = 1,
pages = 117,
doi = {10.1186/s13059-019-1720-5},
}

@article{alkan2011genome,
title={Genome structural variation discovery and genotyping},
author={Alkan, Can and Coe, Bradley P and Eichler, Evan E},
journal={Nature Reviews Genetics},
volume={12},
number={5},
pages={363},
year={2011},
publisher={Nature Publishing Group}
title = {Genome structural variation discovery and genotyping},
author = {Alkan, Can and Coe, Bradley P and Eichler, Evan E},
year = 2011,
journal = {Nature Reviews Genetics},
publisher = {Nature Publishing Group},
volume = 12,
number = 5,
pages = 363,
doi = {10.1038/nrg2958},
}

@article{alves2013gene,
title={Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line},
author={Alves, In{\^e}s Teles and Hiltemann, Saskia and Hartjes, Thomas and van der Spek, Peter and Stubbs, Andrew and Trapman, Jan and Jenster, Guido},
journal={Human genetics},
volume={132},
number={6},
pages={709--713},
year={2013},
publisher={Springer}
title = {Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line},
author = {Alves, In{\^e}s Teles and Hiltemann, Saskia and Hartjes, Thomas and van der Spek, Peter and Stubbs, Andrew and Trapman, Jan and Jenster, Guido},
year = 2013,
journal = {Human genetics},
publisher = {Springer},
volume = 132,
number = 6,
pages = {709--713},
doi = {10.1007/s00439-013-1308-1},
}
@article{Rasche_2020,
title = {Galactic Circos: User-friendly Circos plots within the Galaxy platform},
author = {Rasche, Helena and Hiltemann, Saskia},
year = 2020,
month = jun,
journal = {GigaScience},
publisher = {Oxford University Press (OUP)},
volume = 9,
number = 6,
doi = {10.1093/gigascience/giaa065},
issn = {2047-217x},
url = {http://dx.doi.org/10.1093/gigascience/giaa065},
}

2 changes: 1 addition & 1 deletion topics/visualisation/tutorials/circos/tutorial.md
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---


Circos ({% cite krzywinski2009circos %}) is a software package for visualizing data in a circular layout. This makes Circos ideal for exploring relationships between objects or positions. Circos plots have appeared in thousands of scientific publications. Although originally designed for visualizing genomic data, it can create figures from data in any field.
Circos ({% cite krzywinski2009circos %}) is a software package for visualizing data in a circular layout. This makes Circos ideal for exploring relationships between objects or positions. Circos plots have appeared in thousands of scientific publications. Although originally designed for visualizing genomic data, it can create figures from data in any field. In this tutorial we discuss the Galactic Circos ({% cite Rasche_2020 %}) tool which enables you to access Circos via the convenient Galaxy interface, and even produce plots as part of your workflows!

![Panel of example Circos images](../../images/circos-sample-panel.png)

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