getdifferentialexpression

getdifferentialexpression performs differential expression analysis between two conditions using Fisher's exact test on genomic regions defined by an external file to identify region-specific expression changes.

Key Features:

• Differential Expression Using Fisher's Exact Test: Applies Fisher's exact test to compare expression counts between two conditions, appropriate for small sample sizes and discrete count data.
• Region-Specific Analysis: Accepts an external file specifying genomic regions (for example promoters or enhancers) to restrict analysis to defined loci.
• Next-Generation Sequencing Compatibility: Operates on count data generated from next-generation sequencing technologies.
• Reproducibility and Provenance Tracking: Records analysis details including data provenance, parameter settings, and workflow steps.

Scientific Applications:

• Disease Mechanism Studies: Identifying gene expression changes between conditions to investigate disease mechanisms.
• Treatment Response Analysis: Assessing expression changes associated with treatment responses.
• Developmental Biology: Comparing condition-dependent expression across developmental processes.
• Regulatory Element Discovery: Detecting region-specific regulatory elements, such as promoters and enhancers, that influence expression differences.

Methodology:

Applies Fisher's exact test to expression counts within genomic regions provided via an external file to assess statistical significance between two conditions.