doseR

doseR detects directional shifts in gene expression among pre-defined groups of loci from next generation sequencing count data, with primary application to sex chromosome dosage compensation analysis.

Key Features:

• Differential expression analysis: Detects directional shifts in expression for multiple, specific subsets of genes from count data.
• Data management: Uses S4 classes to store count data from sequencing experiments.
• Normalization and filtering: Contains functions to normalize and filter count data.
• Visualization and statistics: Provides functions to plot and calculate statistics of count data.
• Linear modeling framework: Contains a framework for linear modeling of count data.

Scientific Applications:

• Sex chromosome dosage compensation: Analyzes dosage compensation in sex chromosomes using next generation sequencing data.
• Systems biology research: Enables broad utility for detecting expression shifts across arbitrary pre-defined gene groups in systems biology contexts.

Methodology:

The package uses S4 classes for data storage and implements linear modeling of count data, with validation using real and simulated data.