RomicsProcessor

RomicsProcessor is an R package for analyzing bulk, single-cell, and spatial omics dataesets. The package provides a structured R object (romics_object) to store data, metadata, and processing history, enabling reproducible and FAIR-compatible data analysis. RomicsProcessor also supports creating reusable analytical pipelines from previously processed objects, allowing for rapid development and method reuse.

Version 1.17.0 adds comprehensive format conversion capabilities, including seamless interoperability with Seurat objects and SpatialExperiment formats, alongside enhanced spatial analysis and embeddings support.

Key Features

• Multi-Omics Support: Handle bulk, single-cell, and spatial omics datasets (proteomics, metabolomics, genomics, etc.)
• Reproducible Analysis: Full processing history tracking with audit trail ensures complete reproducibility
• FAIR Compliant: Encapsulated romics_objects ensure Findability, Accessibility, Interoperability, and Reusability
• Format Interoperability: Seamless conversion with Seurat objects and SpatialExperiment for ecosystem integration
• Large-Scale Spatial Data: Optimized for hundreds of thousands of data points (multiplexed immunofluorescence, MSI)
• Spatial Map Generation: Interactive visualization of spatial coordinates with feature overlays, clustering patterns, and factor-based coloring
• Comprehensive Analysis: Data import/transformation, normalization, dimensionality reduction, clustering, statistical analysis
• Advanced Visualization: Interactive Shiny web interfaces, publication-quality plots, and interactive spatial maps
• Batch Correction: Combat/SVA methods for multi-batch omics integration

Recent Improvements (v1.17.0)

• 🔄 Format Conversion: Convert between Seurat objects and romics_objects bidirectionally (SeuratToRomics, romicsToSeurat)
• 🗺️ Spatial Integration: Export romics_objects to SpatialExperiment format for BANKSY spatial analysis
• 📍 Embedding Import: Automatic PCA, UMAP, and other dimensional reductions preserved during conversions
• 🚀 Performance: Optimized metadata handling and vectorized matrix operations
• 📝 Documentation: Enhanced roxygen documentation with improved formatting and clarity

Installation

Prerequisites

install.packages(“devtools”)

Install from GitHub

devtools::install_github(“PNNL-Comp-Mass-Spec/RomicsProcessor”)

Optional Bioconductor Dependencies

For enhanced functionality, install these optional packages:

# For batch correction (Combat/SVA method)
BiocManager::install(“sva”)

# For advanced omics utilities
install.packages(“pmartR”)

# For ComplexHeatmap and advanced visualization
BiocManager::install(“ComplexHeatmap”)

System Requirements

• R: ≥ 4.0.0
• Memory: For large datasets (>100k samples), recommend ≥16GB RAM
  • Use dimensionally reduced data (PCA/UMAP) with reduced k parameter for memory efficiency

Example of use

The folder /Example contain an example romics_objeft

Cite the code

To cite the package please use the following DOI:

Authors

Geremy Clair (main contact) - geremy.clair@pnnl.gov
Harsh Bhotika - harsh.bhotika@pnnl.gov
Brittney Gorman - brittney.gorman@pnnl.gov

Written for the Department of Energy (PNNL, Richland, WA)
Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/
E-mail: proteomics@pnnl.gov

License

RomicsProcessor is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2019 Battelle Memorial Institute