VisRseq: R-based visual framework for analysis of sequencing data

BMC Bioinformatics

Volumn 16, Issue 11, 2015, Pages

  Younesy, Hamid ^a,b,d   Möller, Torsten ^a,c   Lorincz, Matthew C ^d   Karimi, Mohammad M ^d   Jones, Steven J M ^a,b,d  

^a SIMON FRASER UNIVERSITY   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c UNIVERSITY OF VIENNA   (Austria)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Interactive Visualization; R project; Sequencing Data

Indexed keywords

GRAPHICAL USER INTERFACES; USER INTERFACES; VISUALIZATION;

COMPUTATIONAL PACKAGE; COMPUTATIONAL TOOLS; GENOME BROWSERS; INTERACTIVE ANALYSIS; INTERACTIVE VISUALIZATIONS; INTERACTIVITY; R-PROJECT; SEQUENCING DATA;

DATA VISUALIZATION;

CASE REPORT; COMPUTER INTERFACE; GENOME; HUMAN; LIBRARY; WORKFLOW; ANIMAL; BIOLOGY; C57BL MOUSE; COMPUTER GRAPHICS; DNA SEQUENCE; EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENE FREQUENCY; GERM CELL; HIGH THROUGHPUT SEQUENCING; INTERNET; METABOLISM; MOUSE; NUCLEIC ACID DATABASE; PROCEDURES; SOFTWARE; TROPHOBLAST;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, NUCLEIC ACID; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENOME; GERM CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; MICE; MICE, INBRED C57BL; SEQUENCE ANALYSIS, DNA; SOFTWARE; TROPHOBLASTS; USER-COMPUTER INTERFACE; WORKFLOW;

EID: 84961575432     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-16-S11-S2     Document Type: Article

References (60)

1. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al: Bioconductor: open software development for computational biology and bioinformatics. Genome Biology. 2004, 5 (10): 80-10.1186/gb-2004-5-10-r80.
2. Ihaka R, Gentleman R: R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics. 1996, 5 (3): 299-314.
3. Meyer M, Munzner T, Pfister H: MizBee: a multiscale synteny browser. IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis 2009). 2009, 15 (6): 897-904.
4. Meyer M, Wong B, Styczynski M, Munzner T, Pfister H: Pathline: A tool for comparative functional genomics. Computer Graphics Forum. 2010, Wiley Online Library, 29: 1043-1052. 10.1111/j.1467-8659.2009.01710.x.
5. Younesy H, Nielsen CB, Möller T, Alder O, Cullum R, Lorincz MC, Karimi MM, Jones SJ: An interactive analysis and exploration tool for epigenomic data. Computer Graphics Forum. 2013, Wiley Online Library, 32: 91-100. 10.1111/cgf.12096.
6. Schroeder W, Martin K, Lorensen B: Visualization Toolkit: An object-oriented approach to 3D graphics. 2006, Kitware
7. Heer J, Card SK, Landay JA: Prefuse: a toolkit for interactive information visualization. Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. 2005, ACM, 421-430.
8. Stolte C, Tang D, Hanrahan P: Polaris: A system for query, analysis, and visualization of multidimensional relational databases. IEEE Transactions on Visualization and Computer Graphics. 2002, 8 (1): 52-65. 10.1109/2945.981851.
9. Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B: KNIME: The Konstanz information miner. Data Analysis, Machine Learning and Applications. 2008, Springer, Freiburg, Germany, 319-326.
10. Demšar J, Zupan B, Leban G, Curk T: Orange: From experimental machine learning to interactive data mining. European Conference of Machine Learning. 2004, Springer, Pisa, Italy, 537-539.
11. Satyanarayan A, Heer J: Lyra: An interactive visualization design environment. Computer Graphics Forum. 2014, Wiley Online Library, 33: 351-360.
12. CSIRO Workspace. Accessed: 2015-4-15, [ https://research.csiro.au/workspace/ ]
13. Lawrence M, Temple Lang D: RGtk2: A graphical user interface toolkit for R. Journal of Statistical Software. 2010, 37 (8): 1-52.
14. Hoffmann TJ, Laird NM: fgui: A method for automatically creating graphical user interfaces for command-line R packages. Journal of Statistical Software. 2004, 30 (2): 1-14.
15. Dalgaard P: The R-Tcl/Tk interface. Proceedings of the 2nd International Workshop on Distributed Statistical Computing. 2011, 2-
16. Verzani J: An introduction to gWidgets. R News. 2007, 3 (3): 26-33.
17. Helbig M, Theus M, Urbanek S: JGR: Java GUI for R. Statistical Computing and Graphics Newsletter. 2005, 16 (2): 9-12.
18. SciViews-R: A GUI API for R. Mons, Belgium. Accessed: 2015-2-15, [ http://www.sciviews.org/SciViews-R ]
19. Fellows I: Deducer: A data analysis gui for R. Journal of Statistical Software. 2012, 49 (8): 1-15.
20. Fox J: Getting started with the R commander: a basic-statistics graphical user interface to R. Journal of Statistical Software. 2005, 14 (9): 1-42.
21. Hervé M: GrapheR: a multiplatform GUI for drawing customizable graphs in R. The R Journal. 2011, 3 (2): 45-53.
22. Williams GJ: Data mining with Rattle and R: The art of excavating data for knowledge discovery. 2011, Springer
23. Novák P, Neumann P, Macas J: Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC bioinformatics. 2010, 11 (1): 378-10.1186/1471-2105-11-378.
24. Wettenhall JM, Smyth GK: limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics. 2004, 20 (18): 3705-3706. 10.1093/bioinformatics/bth449.
25. Wettenhall JM, Simpson KM, Satterley K, Smyth GK: affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics. 2006, 22 (7): 897-899. 10.1093/bioinformatics/btl025.
26. Futschik ME, Crompton T: OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics. 2005, 21 (8): 1724-1726. 10.1093/bioinformatics/bti199.
27. Shiny by RStudio. Accessed: 2015-2-15, [ http://shiny.rstudio.com ]
28. ggvis 0.4. Accessed: 2015-2-15, [ http://ggvis.rstudio.com ]
29. Gesmann M, de Castillo D: Using the Google visualisation API with R. The R Journal. 2011, 3 (2): 40-44.
30. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Research. 2002, 12 (6): 996-1006. 10.1101/gr.229102. Article published online before print in May 2002.
31. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nature Biotechnology. 2011, 29 (1): 24-26. 10.1038/nbt.1754.
32. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology. 2008, 26 (11): 1293-1300. 10.1038/nbt.1505.
33. Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L: seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Research. 2011, 39 (6): 35-35. 10.1093/nar/gkq1287.
34. Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, et al: Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology. 2011, 12 (8): 83-10.1186/gb-2011-12-8-r83.
35. Halachev K, Bast H, Albrecht F, Lengauer T, Bock C: EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology. 2012, 13 (10): 96-10.1186/gb-2012-13-10-r96.
36. Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, et al: The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biology. 2010, 11 (12): 121-10.1186/gb-2010-11-12-r121.
37. FlowJo Software. Accessed: 2015-2-15, [ http://www.flowjo.com ]
38. SeqMonk Software. Accessed: 2015-2-15, [ http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ]
39. Chelaru F, Smith L, Goldstein N, Bravo HC: Epiviz: interactive visual analytics for functional genomics data. Nature Methods. 2014, 11 (9): 938-940. 10.1038/nmeth.3038.
40. Goecks J, Nekrutenko A, Taylor J, The Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology. 2010, 11 (8): 86-10.1186/gb-2010-11-8-r86.
41. Sedlmair M, Meyer M, Munzner T: Design study methodology: Reflections from the trenches and the stacks. IEEE Transactions on Visualization and Computer Graphics. 2012, 18 (12): 2431-2440.
42. WireframeSketcher: wireframing tool for professionals. Accessed: 2015-2-15, [ http://wireframesketcher.com ]
43. Rserve - Binary R server. Accessed: 2015-2-15, [ http://rforge.net/Rserve/ ]
44. RStudio: Integrated development environment for R (version 0.98.1102). Accessed: 2015-2-15, [ http://www.rstudio.org ]
45. Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biology. 2010, 11 (10): 106-10.1186/gb-2010-11-10-r106.
46. Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD: Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols. 2013, 8 (9): 1765-1786. 10.1038/nprot.2013.099.
47. Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010, 26 (1): 139-140. 10.1093/bioinformatics/btp616.
48. 3 data-driven documents. IEEE Transactions on Visualization and Computer Graphics. 2011, 17 (12): 2301-2309.
49. Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Ayllón NDT, et al: BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 2013, 29 (8): 1103-1104. 10.1093/bioinformatics/btt100.
50. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, et al: The sequence alignment/map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
51. UCSC Genome Bioinformatics - Wiggle Track Format. Accessed: 2015-4-15, [ http://genome.ucsc.edu/goldenPath/help/wiggle ]
52. Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, et al: DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell. 2011, 8 (6): 676-687. 10.1016/j.stem.2011.04.004.
53. Liu S, Brind'Amour J, Karimi MM, Shirane K, Bogutz A, Lefebvre L, Sasaki H, Shinkai Y, Lorincz MC: Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells. Genes & Development. 2014, 28 (18): 2041-2055. 10.1101/gad.244848.114.
54. Maksakova IA, Thompson PJ, Goyal P, Jones SJ, Singh PB, Karimi MM, Lorincz MC: Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics & Chromatin. 2013, 6 (1): 15-10.1186/1756-8935-6-15.
55. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
56. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. 1995, 57 (1): 289-300.
57. Calabrese JM, Sun W, Song L, Mugford JW, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford GE, Magnuson T: Site-specific silencing of regulatory elements as a mechanism of × inactivation. Cell. 2012, 151 (5): 951-963. 10.1016/j.cell.2012.10.037.
58. Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJM: ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014, 30 (8): 1172-1174. 10.1093/bioinformatics/btt744.
59. Morison IM, Reeve AE: A catalogue of imprinted genes and parent-of-origin effects in humans and animals. Human Molecular Genetics. 1998, 7 (10): 1599-1609. 10.1093/hmg/7.10.1599.
60. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007, 448 (7153): 553-560. 10.1038/nature06008.