Panpipes

Panpipes automates multimodal single-cell and spatial transcriptomic analyses by incorporating widely used Python-based tools for quality control, preprocessing, integration, clustering, and reference mapping at scale.

Key Features:

• Quality Control and Preprocessing: Performs quality control and preprocessing for multimodal single-cell and spatial transcriptomic data.
• Integration: Enables integration of individual and multiple modalities for joint evaluation.
• Clustering: Performs clustering analysis on single-cell and spatial transcriptomic datasets.
• Reference Mapping: Supports reference mapping for cell identification and annotation.
• Customizable Analysis: Allows reliable and customizable analysis and evaluation of individual and integrated modalities.

Scientific Applications:

• Multiomic Single-Cell Analysis: Analyzes epigenome, transcriptome, and proteome data for comprehensive characterization of molecular circuitry underlying cell identity and state.
• Spatial Transcriptomics: Processes and analyzes spatial transcriptomic data to investigate tissue architecture and gene expression patterns.
• Joint Modality Evaluation: Enables systematic, joint evaluation of different modalities for holistic interpretation of multiomic datasets.
• Downstream Decision Support: Empowers decision-making before downstream investigations through reliable analysis and evaluation of integrated modalities.

Methodology:

Panpipes incorporates widely used Python-based tools into computational workflows.