multiROMA

Representation and Quantification of Module Activity in multi-omic data

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Features

• Compute module activity scores for single-cell and bulk dataset with RNA-seq and proteomic data
• Seamless integration with AnnData objects (scanpy)
• Support for GMT pathway files (e.g., MSigDB hallmark gene sets)

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Installation

Install directly from source

git clone https://github.com/Lucie-Garance/multiROMA.git
cd pyroma
pip install -e .

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Quick Start

import roma_gsvd_v2 as Roma

# Initialize ROMA
roma = Roma.ROMA()

# Assign your AnnData object and GMT file
roma.adata = adata  # AnnData from scanpy
roma.gmt   = my_gmt_path

# Compute module activity scores
roma.compute()

# Inspect results
roma.adata.uns['ROMA_active_modules']

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Tutorials

Comprehensive notebooks are available:

• Preprocessing dataset: Data_preprocessing.ipynb
• MFA method: MFA_multiROMA.ipynb
• GSVD method: GSVD_multiROMA.ipynb

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Reproducibility

Companion notebooks and detailed workflows will be available soon. For any detailed information, please contact lucie.garance.barot@gmail.com

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References

1. Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A (2016). ROMA: Representation and Quantification of Module Activity from Target Expression Data. Front. Genet. 7:18.
2. Najm M, Cornet M, Albergante L, et al. (2024). Representation and quantification of module activity from omics data with rROMA. npj Syst Biol Appl. 10:8.