systemPipeR

systemPipeR automates construction and execution of reproducible next-generation sequencing (NGS) analysis workflows for applications including RNA-Seq, ChIP-Seq, VAR-Seq, and Ribo-Seq.

Key Features:

• End-to-End Workflow Automation: Facilitates construction and execution of automated workflows for NGS applications including RNA-Seq, ChIP-Seq, VAR-Seq, and Ribo-Seq.
• Integration of R and Command-Line Tools: Supports execution of R/Bioconductor code alongside external command-line software within workflows.
• Automated Report Generation: Produces automated reports that document analysis steps and results.
• Scalability Across Computing Environments: Executes workflows on local computers and on compute clusters.
• Flexible Sample Annotation Infrastructure: Manages complex sample sets and experimental designs via adaptable annotation structures.
• Pre-configured Workflows and Templates: Provides pre-configured workflow and reporting templates tailored to common NGS applications.
• Extensibility: Designed to be extensible for additional workflow templates and future applications.

Scientific Applications:

• Transcriptomics: Supports analysis of RNA-Seq and Ribo-Seq data.
• Epigenetics: Supports analysis of ChIP-Seq data.
• Variant analysis: Supports analysis of VAR-Seq data.
• Genomics: Supports general genomics studies using automated NGS workflows.
• Proteomics: Supports proteomics-related analyses referenced in NGS workflow contexts.

Methodology:

Implements automated workflow construction and execution as an R/Bioconductor package, runs R-based analyses and external command-line software, uses a sample annotation infrastructure, generates automated reports, and supports execution on local machines and compute clusters.