expVIP

expVIP provides visualization and integration of RNA-seq expression data to enable transcriptome analyses and comparative expression studies in plants, including polyploid crops such as wheat (Triticum aestivum).

Key Features:

• Disparate transcriptome reference handling: Supports integration and comparison of RNA-seq data across disparate transcriptome references.
• Differential gene expression analysis outputs: Produces outputs tailored to facilitate differential gene expression analysis from RNA-seq datasets.
• Virtual machine-based deployment: Deployable within a virtual machine environment to provide a contained analysis and data integration environment.
• Flexible data integration: Enables incorporation of user-generated data into existing expression datasets.
• Cross-experiment comparison and visualization: Enables comparison and visualization of RNA-seq data across multiple experiments.
• Polyploid crop suitability: Demonstrated applicability to polyploid crops, exemplified by use in wheat (Triticum aestivum).

Scientific Applications:

• Wheat and crop transcriptomics: Applied to wheat research and implemented as a flexible expression browser (www.wheat-expression.com) for crop gene expression studies.
• Comparative and integrative transcriptomics: Supports cross-experiment and cross-species expression comparisons for broader transcriptome investigations.

Methodology:

Operates using a virtual machine-based environment with visualization tools, generates outputs for differential gene expression analysis, and supports integration of user-supplied RNA-seq datasets.