epidecodeR

epidecodeR analyses the impact of varying degrees of DNA/RNA epigenetic chemical modifications on gene or protein dysregulation by integrating epigenomic or epitranscriptomic modification data with differential expression, ribosome occupancy, or protein translation data.

Key Features:

• Multi-technique data integration: Integrates chemical modification data from ChIP-seq, ATAC-seq, m6A-seq, and other epigenomic or epitranscriptomic techniques.
• Dysregulation analysis: Identifies the impact of gene dysregulation caused by varying degrees of chemical modifications associated with genes.
• Cumulative distribution function plotting: Generates CDF plots showing shifts in overall log2FC trends between genes grouped by degree of modification.
• Statistical significance testing: Tests for significance of difference in log2FC between groups of genes.

Scientific Applications:

• Epigenetic regulation analysis: Analyses how DNA epigenetic chemical modifications impact gene or protein dysregulation.
• Epitranscriptomic regulation analysis: Analyses how RNA epigenetic chemical modifications impact gene or protein dysregulation.
• Differential gene expression integration: Integrates differential gene expression data with modification data to identify regulatory impacts.
• Ribosome occupancy integration: Integrates ribosome occupancy data with modification data to identify translational regulatory impacts.
• Differential protein translation integration: Integrates differential protein translation data with modification data to identify protein-level regulatory impacts.

Methodology:

epidecodeR divides genes into groups based on the degree of chemical modification associated with the genes, generates cumulative distribution function plots showing shifts in trend of overall log2FC between these groups, and tests for significance of difference in log2FC between groups of genes.