ggbio: an R package for extending the grammar of graphics for genomic data

被引：223
作者：
Yin, Tengfei [1 ]
Cook, Dianne [2 ]
Lawrence, Michael [3 ]
机构：
[1] Iowa State Univ, Dept Genet Dev & Cell Biol, Ames, IA 50011 USA
[2] Iowa State Univ, Dept Stat, Ames, IA 50011 USA
[3] Genentech Inc, Dept Bioinformat, San Francisco, CA 94080 USA
来源：
GENOME BIOLOGY | 2012年 / 13卷 / 08期
关键词：
BROWSER; VISUALIZATION; EXPLORATION; SOFTWARE;
D O I：
10.1186/gb-2012-13-8-r77
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html.
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页数：14
相关论文
共 34 条
  • [1] Aboyoun P., GENOMICRANGES REPRES
  • [2] A haplotype map of the human genome
    Altshuler, D
    Brooks, LD
    Chakravarti, A
    Collins, FS
    Daly, MJ
    Donnelly, P
    Gibbs, RA
    Belmont, JW
    Boudreau, A
    Leal, SM
    Hardenbol, P
    Pasternak, S
    Wheeler, DA
    Willis, TD
    Yu, FL
    Yang, HM
    Zeng, CQ
    Gao, Y
    Hu, HR
    Hu, WT
    Li, CH
    Lin, W
    Liu, SQ
    Pan, H
    Tang, XL
    Wang, J
    Wang, W
    Yu, J
    Zhang, B
    Zhang, QR
    Zhao, HB
    Zhao, H
    Zhou, J
    Gabriel, SB
    Barry, R
    Blumenstiel, B
    Camargo, A
    Defelice, M
    Faggart, M
    Goyette, M
    Gupta, S
    Moore, J
    Nguyen, H
    Onofrio, RC
    Parkin, M
    Roy, J
    Stahl, E
    Winchester, E
    Ziaugra, L
    Shen, Y
    [J]. NATURE, 2005, 437 (7063) : 1299 - 1320
  • [3] A map of human genome variation from population-scale sequencing
    Altshuler, David
    Durbin, Richard M.
    Abecasis, Goncalo R.
    Bentley, David R.
    Chakravarti, Aravinda
    Clark, Andrew G.
    Collins, Francis S.
    De la Vega, Francisco M.
    Donnelly, Peter
    Egholm, Michael
    Flicek, Paul
    Gabriel, Stacey B.
    Gibbs, Richard A.
    Knoppers, Bartha M.
    Lander, Eric S.
    Lehrach, Hans
    Mardis, Elaine R.
    McVean, Gil A.
    Nickerson, DebbieA.
    Peltonen, Leena
    Schafer, Alan J.
    Sherry, Stephen T.
    Wang, Jun
    Wilson, Richard K.
    Gibbs, Richard A.
    Deiros, David
    Metzker, Mike
    Muzny, Donna
    Reid, Jeff
    Wheeler, David
    Wang, Jun
    Li, Jingxiang
    Jian, Min
    Li, Guoqing
    Li, Ruiqiang
    Liang, Huiqing
    Tian, Geng
    Wang, Bo
    Wang, Jian
    Wang, Wei
    Yang, Huanming
    Zhang, Xiuqing
    Zheng, Huisong
    Lander, Eric S.
    Altshuler, David L.
    Ambrogio, Lauren
    Bloom, Toby
    Cibulskis, Kristian
    Fennell, Tim J.
    Gabriel, Stacey B.
    [J]. NATURE, 2010, 467 (7319) : 1061 - 1073
  • [4] Detecting differential usage of exons from RNA-seq data
    Anders, Simon
    Reyes, Alejandro
    Huber, Wolfgang
    [J]. GENOME RESEARCH, 2012, 22 (10) : 2008 - 2017
  • [5] [Anonymous], LATTICE LATTICE GRAP
  • [6] [Anonymous], STAT COMPUTING
  • [7] [Anonymous], J COMPUT GRAPHICAL S
  • [8] [Anonymous], WILEY INTERDISCIPLIN
  • [9] Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    Bass, Adam J.
    Lawrence, Michael S.
    Brace, Lear E.
    Ramos, Alex H.
    Drier, Yotam
    Cibulskis, Kristian
    Sougnez, Carrie
    Voet, Douglas
    Saksena, Gordon
    Sivachenko, Andrey
    Jing, Rui
    Parkin, Melissa
    Pugh, Trevor
    Verhaak, Roel G.
    Stransky, Nicolas
    Boutin, Adam T.
    Barretina, Jordi
    Solit, David B.
    Vakiani, Evi
    Shao, Wenlin
    Mishina, Yuji
    Warmuth, Markus
    Jimenez, Jose
    Chiang, Derek Y.
    Signoretti, Sabina
    Kaelin, William G., Jr.
    Spardy, Nicole
    Hahn, William C.
    Hoshida, Yujin
    Ogino, Shuji
    DePinho, Ronald A.
    Chin, Lynda
    Garraway, Levi A.
    Fuchs, Charles S.
    Baselga, Jose
    Tabernero, Josep
    Gabriel, Stacey
    Lander, Eric S.
    Getz, Gad
    Meyerson, Matthew
    [J]. NATURE GENETICS, 2011, 43 (10) : 964 - U67
  • [10] DNAPlotter: circular and linear interactive genome visualization
    Carver, Tim
    Thomson, Nick
    Bleasby, Alan
    Berriman, Matthew
    Parkhill, Julian
    [J]. BIOINFORMATICS, 2009, 25 (01) : 119 - 120
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