systemPipeShiny

systemPipeShiny extends the systemPipeR workflow environment with interactive workflow design, control, and visualization functionalities for data analysis pipelines in the R/Bioconductor ecosystem.

Key Features:

• Interactive Experimental Design: Creation of experimental designs and metadata using a tabular editor or file uploader.
• Workflow Topology Visualization: Visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows.
• Data Processing Routines: Access to a wide range of data processing routines.
• Visualization Suite: Pre-configured visualization examples including PCA, t-SNE, clustering methods, volcano plots, and heatmaps for count table data.
• Canvas Workbench: Management of complex visual results with organization, comparison of plots, and session snapshot features.
• Modular Framework Integration: General purpose framework for interacting with other R packages and integrating core packages from the R/Bioconductor ecosystem.

Scientific Applications:

• Workflow Management: Interactive design, control, and execution of systemPipeR workflows for computational biology pipelines.
• Dimensionality Reduction Analysis: PCA and t-SNE visualization of count table data for exploratory data analysis.
• Differential Expression Visualization: Volcano plot generation for displaying differential expression results.
• Clustering Analysis: Heatmap generation and other clustering method visualizations for data mining.

Methodology:

systemPipeShiny provides a Shiny App graphical interface to systemPipeR workflows, with modular design enabling custom function development and integration with R/Bioconductor packages.