systemPipeTools

systemPipeTools extends the systemPipeR workflow environment with an enhanced toolkit for data visualization and automated analysis of differentially expressed genes.

Key Features:

• Differential Expression Visualization: Automates data visualization for analysis of differentially expressed genes.
• Data Transformation: Provides data transformation functions for downstream analysis and visualization.
• Dimensionality Reduction: Supports principal component analysis, multidimensional scaling, generalized principal components, and t-Distributed Stochastic Neighbor embedding.
• Exploratory Plotting: Generates scatterplots, hierarchical clustering heatmaps, MA plots, and volcano plots.
• Modular Integration: Utilities integrate with the systemPipeR environment allowing substitution with custom alternatives.

Scientific Applications:

• Gene Expression Analysis: Visualizes results from differentially expressed gene analysis workflows.
• Transcriptomics Data Exploration: Enables exploratory analysis of high-throughput gene expression data through multiple visualization methods.
• Workflow Integration: Extends systemPipeR workflows with standardized, interchangeable visualization components.

Methodology:

systemPipeTools provides data transformation and exploration functions implemented as modular components within the systemPipeR environment.