eisaR

eisaR implements exon-intron split analysis (EISA) in R to quantify transcriptional and post-transcriptional regulation of gene expression from ordinary RNA-seq data by measuring changes in mature RNA and pre-mRNA reads across experimental conditions.

Key Features:

• Exon-intron split analysis: Measures changes in mature RNA (exonic reads) and pre-mRNA (intronic reads) across different experimental conditions.
• Transcriptional regulation quantification: Uses intronic read counts to accurately predict changes in transcriptional activity based on nuclear RNA-derived reads.
• Post-transcriptional regulation quantification: Predicts changes in post-transcriptional regulation from differences between exonic and intronic changes.

Scientific Applications:

• Gene expression regulation analysis: Distinguishes transcriptional and post-transcriptional contributions to expression changes in RNA-seq data sets.
• Diverse data set analysis: Applicable to diverse RNA-seq data sets to extract additional regulatory information beyond standard expression analysis.

Methodology:

eisaR implements the major steps of EISA in R, using ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions.