vidger

vidger provides R/Bioconductor functions that generate visualizations to facilitate interpretation of differential gene expression (DGE) results from RNA-seq analyses.

Key Features:

• R/Bioconductor implementation: Implements visualization functions as an R/Bioconductor package.
• Input compatibility: Accepts DGE outputs from Cuffdiff, DESeq2, and edgeR.
• Visualization types: Produces volcano plots, MA plots, heatmaps, and other functional summaries.
• Analytical emphasis: Highlights significantly regulated genes, evaluates data quality, and displays global transcriptomic trends.
• Cross-species evaluation: Has been evaluated on human, Malus domestica, and Vitis riparia DGE datasets.

Scientific Applications:

• Differential expression interpretation: Facilitates interpretation of RNA-seq DGE results to identify differentially expressed genes.
• Data quality assessment: Supports evaluation of data quality and assessment of statistical outputs from DGE analyses.
• Transcriptomic trend exploration: Enables exploration of global transcriptomic patterns across conditions and organisms including human, Malus domestica, and Vitis riparia.
• Biological discovery: Standardizes visualization to support discovery from transcriptomic datasets.

Methodology:

Generates volcano plots, MA plots, heatmaps, and functional summaries from DGE result objects produced by Cuffdiff, DESeq2, and edgeR within R/Bioconductor.