CNPS.cycle

CNPS.cycle streamlines the analysis of shotgun metagenomic data related to carbon, nitrogen, phosphorus, and sulfur biogeochemical cycles through automated data processing, curation, differential analysis, and visualization.

Key Features:

• Four analysis modules: Dedicated modules for carbon, nitrogen, phosphorus, and sulfur cycling.
• Automated data preprocessing and curation: Processes annotation result files from shotgun metagenomic data.
• Differential analysis of biogeochemical cycle-related genes: Identifies differentially abundant genes associated with elemental cycles.
• Contig-level microbial analysis: Analyzes microorganisms possessing biogeochemical cycle-related genes at the contig level.
• Beta-diversity analysis: Performs beta-diversity analysis of biogeochemical cycle-related genes and microbes.
• Data visualization: Generates tables and high-quality images for comprehensive results presentation.
• Database compatibility: Accepts annotation files based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database.

Scientific Applications:

• Soil ecosystem research: Provides insights into the relationship between soil microorganisms and elemental chemical cycles.
• Environmental management: Supports informed decisions through analysis of microbial-mediated nutrient cycling.
• Climate change mitigation research: Enhances understanding of microbial contributions to ecosystem functions and global biogeochemical processes.

Methodology:

CNPS.cycle is implemented as an R package that automates data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; beta-diversity analysis; and data visualization from user-uploaded annotation result files.