ngsReports

ngsReports parses FastQC reports and output summaries from other NGS tools into R for quality control visualization and analysis.

Key Features:

• FastQC Report Parsing: Imports FastQC reports directly into R using dedicated object classes.
• Multi-tool Parsing: Parses output summaries from other NGS tools beyond FastQC.
• Static Visualization: Generates plots as static ggplot objects with default, highly customizable formatting.
• Interactive Visualization: Generates plots as interactive plotly objects.
• Cross-sample Analysis: Enables visualization across many samples with hierarchical clustering to identify outlier libraries.
• Shiny App Integration: Supports display in an interactive shiny application.
• HTML Report Generation: Produces HTML reports for analysis output.

Scientific Applications:

• NGS Quality Control: Manages and visualizes quality control reports from high-throughput next generation sequencing pipelines.
• Systemic Bias Detection: Identifies systemic bias across large sample numbers by inspecting outputs from FastQC and Picard.
• Outlier Library Identification: Detects outlier libraries through hierarchical clustering of quality metrics across samples.

Methodology:

The package implements methods and object classes for parsing FastQC reports and NGS tool output summaries into R, with plotting methods for generating static ggplot objects or interactive plotly objects, and includes hierarchical clustering for outlier detection.