XiP

XiP enables construction, execution, and customization of modular computational workflows for high-throughput genomic and transcriptomic analyses.

Key Features:

• Modular Workflow Construction: Integrates computational components written in R and Java to compose modular pipelines.
• High-Throughput Data Analysis: Manages large-scale genomic datasets and supports execution within grid engine systems.
• Customizable Pipelines and Packaging: Enables creation of customized pipelines that can be encapsulated into packages for sharing and reuse.
• Pre-configured Pipelines and Components: Includes several ready-to-use pipeline flows and approximately 300 computational components.

Scientific Applications:

• Sequence alignment: Supports workflows that perform sequence alignment on genomic and transcriptomic data.
• Variant calling: Supports integration of variant calling analyses within assembled pipelines.
• Gene expression quantification: Supports workflows for quantifying gene expression from transcriptomic data.
• Differential expression analysis: Supports differential expression analysis as part of transcriptomic workflows.
• Genomics and transcriptomics research: Enables high-throughput analyses applicable to personalized medicine, evolutionary biology, and functional genomics.

Methodology:

Integration of computational components implemented in R and Java, execution within grid engine systems, provision of pre-configured pipeline flows and approximately 300 components, and encapsulation of pipelines into packages for sharing.