genomeSidekick

genomeSidekick analyzes RNA-seq, ATAC-seq, and chromatin immunoprecipitation (ChIP) data to identify differentially expressed genes and differentially accessible or occupied chromatin features and to support functional interpretation via Gene Ontology and literature queries.

Key Features:

• Supported data types: Supports analysis of RNA-seq, ATAC-seq, and ChIP datasets.
• Differential feature identification: Generates lists of differentially expressed genes and differentially accessible or occupied chromatin features.
• Interactive visualizations: Produces interactive volcano plots for exploration of differential omics results.
• Gene Ontology analysis: Performs Gene Ontology (GO) analyses locally.
• Literature integration: Queries PubMed for selected genes to retrieve relevant literature.
• Customizability: Allows editing of the underlying R code for custom analyses.

Scientific Applications:

• Epigenomic and transcriptomic analysis: Enables focused analysis of RNA-seq, ATAC-seq, and ChIP experiments to identify candidate genes and regulatory elements.
• Mechanistic hypothesis generation: Supports inference of biological mechanisms underlying observed changes using differential lists, GO analysis, and literature queries.

Methodology:

Generates lists of differentially expressed genes and differentially accessible/occupied chromatin features, creates interactive volcano plots, performs local Gene Ontology analyses, and queries PubMed for selected genes.