VISTA

VISTA streamlines differential expression workflows by wrapping DESeq2 and edgeR into a SummarizedExperiment-based container with consistent metadata for interactive exploration of RNA-seq experiments.

Key Features:

• DESeq2 and edgeR integration: Wraps both differential expression packages into a unified SummarizedExperiment-based container with consistent metadata.
• Visualization utilities: Provides plotting functions for interactive exploration of RNA-seq data.
• MSigDB enrichment helpers: Includes functions to assist with Molecular Signatures Database enrichment analysis.
• Optional deconvolution support: Offers cell type deconvolution capabilities as an optional feature.

Scientific Applications:

• RNA-seq differential expression analysis: Facilitates statistical comparison of gene expression between conditions using established algorithms.
• Functional enrichment analysis: Supports pathway and gene set enrichment using MSigDB collections.
• Cell type composition inference: Enables estimation of cell type proportions through optional deconvolution methods.

Methodology:

VISTA wraps DESeq2 and edgeR into a SummarizedExperiment-based container with consistent metadata.