Poly Pipeline

Poly Pipeline analyzes spatial transcriptomics data with tailored methods for polyploid organisms while maintaining compatibility with any organism and data input type.

Key Features:

• Standard Spatial Analysis: Integrates packages for spatial transcriptomics analysis including clustering, HVG detection, and statistical significance determination with comprehensive output files.
• Anchoring Analysis: Implements a novel anchoring method for determining regions beyond standard clustering analysis.
• Network Analysis: Generates nodes and edges from original data for network analysis.
• Multi HPC Support: Provides full compatibility with PBS and SGE job schedulers for scalable execution on High-Performance Computing environments.
• Data Converter: Converts any input data format to the proper file format required for downstream analysis.

Scientific Applications:

• Polyploid Organism Analysis: Addresses specific challenges in spatial transcriptomics analysis of polyploid organisms such as wheat (Triticum aestivum L.).
• Cross-Species Benchmarking: Successfully processes spatial transcriptomics data from Arabidopsis thaliana, rice (Oryza sativa), and mouse (Mus musculus).

Methodology:

The pipeline integrates a suite of packages for spatial transcriptomics analysis and implements a novel anchoring method for region determination alongside clustering analysis.