polyester

polyester simulates RNA-seq reads to enable benchmarking and development of differential expression analysis methods, including isoform-level changes across biological replicates.

Key Features:

• Simulation of RNA-seq Reads: Simulates RNA-seq reads from differential expression experiments while incorporating biological replicates and variability.
• Isoform-Level Differential Expression: Supports simulation of isoform-level differential expression to model transcript-specific regulation.
• Flexible Experimental Designs: Allows specification of diverse experimental designs and differential expression parameters.
• Realistic Data Approximation: Produces simulated datasets that closely approximate real RNA-seq data so standard differential expression workflows can recover user-defined changes.

Scientific Applications:

• Method development and validation: Benchmarking and validation of statistical methods for RNA-seq differential expression analysis.
• Testing without spike-ins: Generating realistic datasets for method testing without requiring spike-in experiments.
• Controlled evaluations: Creating controlled simulation scenarios to assess accuracy and error rates when true differential expression status is unknown.

Methodology:

Generates RNA-seq reads from user-specified experimental designs and differential expression parameters to produce simulated reads reflecting isoform-level changes across replicates.