xPore

xPore detects and quantifies differential N6-methyladenosine (m6A) RNA modifications from direct RNA sequencing data to enable comparison of modification rates across experimental conditions.

Key Features:

• Single-base resolution identification: Identifies N6-methyladenosine (m6A) sites at single-base resolution from direct RNA sequencing data.
• Quantification of modification fractions: Estimates the fraction of modified RNAs at each site to quantify modification prevalence.
• Differential modification rate analysis: Quantifies differential modification rates across experimental conditions for comparative analyses.
• Joint modification and expression analysis: Performs combined analysis of differential RNA modification and expression levels from the same direct RNA sequencing experiment.
• High accuracy and throughput: Demonstrates high accuracy for identifying RNA modifications and supports transcriptome-wide, high-throughput analysis.

Scientific Applications:

• Transcriptome-wide profiling: Enables transcriptome-wide profiling of m6A modifications using direct RNA sequencing data.
• Comparative cell-line analysis: Applied to direct RNA sequencing data from six cell lines to identify conserved and cell-type–specific m6A sites for comparative and cellular differentiation studies.

Methodology:

Analyzes direct RNA sequencing data to identify m6A sites at single-base resolution, estimate modification fractions, and test for differential modification rates and expression between conditions.