GenVisR: Genomic Visualizations in R

被引：253

作者：

Skidmore, Zachary L. ^{[1
]}

Wagner, Alex H. ^{[1
]}

Lesurf, Robert ^{[1
]}

Campbell, Katie M. ^{[1
]}

Kunisaki, Jason ^{[1
]}

Griffith, Obi L. ^{[1
,2
,3
,4
]}

Griffith, Malachi ^{[1
,3
,4
]}

机构：

[1] Washington Univ, Sch Med, McDonnell Genome Inst, St Louis, MO 63108 USA

[2] Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA

[3] Washington Univ, Sch Med, Siteman Canc Ctr, St Louis, MO 63110 USA

[4] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA

来源：

BIOINFORMATICS | 2016年 / 32卷 / 19期

关键词：

LANDSCAPE; CANCER;

D O I：

10.1093/bioinformatics/btw325

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.

引用

页码：3012 / 3014

页数：3

共 20 条

[1] The landscape of somatic copy-number alteration across human cancers [J].

Beroukhim, Rameen ;

Mermel, Craig H. ;

Porter, Dale ;

Wei, Guo ;

Raychaudhuri, Soumya ;

Donovan, Jerry ;

Barretina, Jordi ;

Boehm, Jesse S. ;

Dobson, Jennifer ;

Urashima, Mitsuyoshi ;

Mc Henry, Kevin T. ;

Pinchback, Reid M. ;

Ligon, Azra H. ;

Cho, Yoon-Jae ;

Haery, Leila ;

Greulich, Heidi ;

Reich, Michael ;

Winckler, Wendy ;

Lawrence, Michael S. ;

Weir, Barbara A. ;

Tanaka, Kumiko E. ;

Chiang, Derek Y. ;

Bass, Adam J. ;

Loo, Alice ;

Hoffman, Carter ;

Prensner, John ;

Liefeld, Ted ;

Gao, Qing ;

Yecies, Derek ;

Signoretti, Sabina ;

Maher, Elizabeth ;

Kaye, Frederic J. ;

Sasaki, Hidefumi ;

Tepper, Joel E. ;

Fletcher, Jonathan A. ;

Tabernero, Josep ;

Baselga, Jose ;

Tsao, Ming-Sound ;

Demichelis, Francesca ;

Rubin, Mark A. ;

Janne, Pasi A. ;

Daly, Mark J. ;

Nucera, Carmelo ;

Levine, Ross L. ;

Ebert, Benjamin L. ;

Gabriel, Stacey ;

Rustgi, Anil K. ;

Antonescu, Cristina R. ;

Ladanyi, Marc ;

Letai, Anthony .

NATURE, 2010, 463 (7283) :899-905

[2] Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].

Chin, L. ;

Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

Mikkelsen, T. ;

VandenBerg, S. ;

Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

[3] Modeling precision treatment of breast cancer [J].

Daemen, Anneleen ;

Griffith, Obi L. ;

Heiser, Laura M. ;

Wang, Nicholas J. ;

Enache, Oana M. ;

Sanborn, Zachary ;

Pepin, Francois ;

Durinck, Steffen ;

Korkola, James E. ;

Griffith, Malachi ;

Hur, Joe S. ;

Huh, Nam ;

Chung, Jongsuk ;

Cope, Leslie ;

Fackler, Mary Jo ;

Umbricht, Christopher ;

Sukumar, Saraswati ;

Seth, Pankaj ;

Sukhatme, Vikas P. ;

Jakkula, Lakshmi R. ;

Lu, Yiling ;

Mills, Gordon B. ;

Cho, Raymond J. ;

Collisson, Eric A. ;

van't Veer, Laura J. ;

Spellman, Paul T. ;

Gray, Joe W. .

GENOME BIOLOGY, 2013, 14 (10)

[4] Organizing knowledge to enable personalization of medicine in cancer [J].

Good, Benjamin M. ;

Ainscough, Benjamin J. ;

McMichael, Josh F. ;

Su, Andrew I. ;

Griffith, Obi L. .

GENOME BIOLOGY, 2014, 15 (08)

[5] Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers [J].

Govindan, Ramaswamy ;

Ding, Li ;

Griffith, Malachi ;

Subramanian, Janakiraman ;

Dees, Nathan D. ;

Kanchi, Krishna L. ;

Maher, Christopher A. ;

Fulton, Robert ;

Fulton, Lucinda ;

Wallis, John ;

Chen, Ken ;

Walker, Jason ;

McDonald, Sandra ;

Bose, Ron ;

Ornitz, David ;

Xiong, Donghai ;

You, Ming ;

Dooling, David J. ;

Watson, Mark ;

Mardis, Elaine R. ;

Wilson, Richard K. .

CELL, 2012, 150 (06) :1121-1134

[6] Genome Modeling System: A Knowledge Management Platform for Genomics [J].

Griffith, Malachi ;

Griffith, Obi L. ;

Smith, Scott M. ;

Ramu, Avinash ;

Callaway, Matthew B. ;

Brummett, Anthony M. ;

Kiwala, Michael J. ;

Coffman, Adam C. ;

Regier, Allison A. ;

Oberkfell, Ben J. ;

Sanderson, Gabriel E. ;

Mooney, Thomas P. ;

Nutter, Nathaniel G. ;

Belter, Edward A. ;

Du, Feiyu ;

Long, Robert L. ;

Abbott, Travis E. ;

Ferguson, Ian T. ;

Morton, David L. ;

Burnett, Mark M. ;

Weible, James V. ;

Peck, Joshua B. ;

Dukes, Adam ;

McMichael, Joshua F. ;

Lolofie, Justin T. ;

Derickson, Brian R. ;

Hundal, Jasreet ;

Skidmore, Zachary L. ;

Ainscough, Benjamin J. ;

Dees, Nathan D. ;

Schierding, William S. ;

Kandoth, Cyriac ;

Kim, Kyung H. ;

Lu, Charles ;

Harris, Christopher C. ;

Maher, Nicole ;

Maher, Christopher A. ;

Magrini, Vincent J. ;

Abbott, Benjamin S. ;

Chen, Ken ;

Clark, Eric ;

Das, Indraniel ;

Fan, Xian ;

Hawkins, Amy E. ;

Hepler, Todd G. ;

Wylie, Todd N. ;

Leonard, Shawn M. ;

Schroeder, William E. ;

Shi, Xiaoqi ;

Carmichael, Lynn K. .

PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (07)

[7] Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia [J].

Gronseth, Christine M. ;

McElhone, Scott E. ;

Storer, Barry E. ;

Kroeger, Kathleen A. ;

Sandhu, Vicky ;

Fero, Matthew L. ;

Appelbaum, Frederick R. ;

Estey, Elihu H. ;

Fang, Min .

CANCER, 2015, 121 (17) :2900-2908

[8] Comprehensive molecular portraits of human breast tumours [J].

Koboldt, Daniel C. ;

Fulton, Robert S. ;

McLellan, Michael D. ;

Schmidt, Heather ;

Kalicki-Veizer, Joelle ;

McMichael, Joshua F. ;

Fulton, Lucinda L. ;

Dooling, David J. ;

Ding, Li ;

Mardis, Elaine R. ;

Wilson, Richard K. ;

Ally, Adrian ;

Balasundaram, Miruna ;

Butterfield, Yaron S. N. ;

Carlsen, Rebecca ;

Carter, Candace ;

Chu, Andy ;

Chuah, Eric ;

Chun, Hye-Jung E. ;

Coope, Robin J. N. ;

Dhalla, Noreen ;

Guin, Ranabir ;

Hirst, Carrie ;

Hirst, Martin ;

Holt, Robert A. ;

Lee, Darlene ;

Li, Haiyan I. ;

Mayo, Michael ;

Moore, Richard A. ;

Mungall, Andrew J. ;

Pleasance, Erin ;

Robertson, A. Gordon ;

Schein, Jacqueline E. ;

Shafiei, Arash ;

Sipahimalani, Payal ;

Slobodan, Jared R. ;

Stoll, Dominik ;

Tam, Angela ;

Thiessen, Nina ;

Varhol, Richard J. ;

Wye, Natasja ;

Zeng, Thomas ;

Zhao, Yongjun ;

Birol, Inanc ;

Jones, Steven J. M. ;

Marra, Marco A. ;

Cherniack, Andrew D. ;

Saksena, Gordon ;

Onofrio, Robert C. ;

Pho, Nam H. .

NATURE, 2012, 490 (7418) :61-70

[9] The sequence read archive: explosive growth of sequencing data [J].

Kodama, Yuichi ;

Shumway, Martin ;

Leinonen, Rasko .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D54-D56

[10] A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML [J].

Krysiak, K. ;

Christopher, M. J. ;

Skidmore, Z. L. ;

Demeter, R. T. ;

Magrini, V. ;

Kunisaki, J. ;

O'Laughlin, M. ;

Duncavage, E. J. ;

Miller, C. A. ;

Ozenberger, B. A. ;

Griffith, M. ;

Wartman, L. D. ;

Griffith, O. L. .

BLOOD CANCER JOURNAL, 2016, 6 :e413-e413

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