9 December 2019

esetVis R package

esetVis

esetVis is an R package to explore and visualize gene expression data provided in ExpressionSet format.

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Advantage: Visualizations for any transcriptomics (e.g. microarray or RNAseq) or proteomics data

esetVis

  • visual exploratory data analysis
  • create plots for specific features
  • identify clusters of biological samples and genes

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esetVis

  • investigate expression profile for a set of genes
  • represent the correlation between genes

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daVis R package

daVis

daVis is an R package to explore and visualize the output from differential expression analysis provided as a list of top tables.

daVis

  • visualize relation between logFC of multiple comparisons
  • investigate overlap of significantly affected genes

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daVis

  • explore the relation between logFC and p-value

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transcriptomicsExplorer ShinyApp

transcriptomicsExplorer

transcriptomicsExplorer is an interactive web application with a user-friendly interface to explore and visualize transcriptomics data.

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transcriptomicsExplorer

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transcriptomicsExplorer

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transcriptomicsExplorer

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Availability

References

  1. H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
  2. Nils Gehlenborg (2019). UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets. R package version 1.4.0. https://CRAN.R-project.org/package=UpSetR
  3. Li X (2019). ALL: A data package. R package version 1.28.0.
  4. Barret Schloerke, Jason Crowley, Di Cook, Francois Briatte, Moritz Marbach, Edwin Thoen, Amos Elberg and Joseph Larmarange (2018). GGally: Extension to 'ggplot2'. R package version 1.4.0. https://CRAN.R-project.org/package=GGally
  5. Orchestrating high-throughput genomic analysis with Bioconductor. W. Huber, V.J. Carey, R. Gentleman, …, M. Morgan Nature Methods, 2015:12, 115.
  6. Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2019). shiny: Web Application Framework for R. R package version 1.3.2. https://CRAN.R-project.org/package=shiny

Thank you for your attention