ProkSeq

ProkSeq performs comprehensive analysis of prokaryotic RNA-seq data to quantify gene expression, detect differential expression across multiple samples, and support pathway enrichment interpretation.

Key Features:

• Automated workflow: Automates processing steps from quality control through pathway enrichment analysis for RNA-seq datasets.
• Quality control and filtering: Performs quality filtering of reads to retain high-quality data for downstream analyses.
• Prokaryote-aware processing: Accounts for prokaryotic gene structure and characteristics in its analyses.
• Differential expression analysis: Detects differential gene expression across multiple samples and experimental conditions.
• Normalization: Implements normalization methods for expression data to enable accurate comparisons across conditions.
• Visualization: Generates visualizations to support interpretation of expression and differential analysis results.
• Pathway enrichment analysis: Links gene expression changes to metabolic or signaling pathways through enrichment analysis.

Scientific Applications:

• Pathogenesis and virulence studies: Analysis of gene expression dynamics in pathogenic bacteria to investigate virulence-related transcriptional changes.
• Stress and environmental response: Examination of transcriptional responses of prokaryotes to varying environmental or extreme conditions.
• Comparative transcriptomics: Comparison of gene expression profiles across multiple samples or conditions to identify regulated genes.
• Microbial systems biology: Integration of expression and pathway-level changes to study microbial metabolism and regulatory networks.

Methodology:

Performs quality control and read filtering, normalizes expression data, conducts differential gene expression analysis across multiple samples, generates visualizations, and performs pathway enrichment analysis.