Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with GPUs
Creators
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1.
University of California, San Francisco
Contributors
Contact person:
-
1.
University of California, San Francisco
Description
Gene expression may be regulated by the DNA methylation of regulatory elements in promoter, gene-body, cis, distal, and trans regions. One method to evaluate the relationship between DNA methylation and gene expression is the mapping of expression quantitative trait methylation (eQTM) loci (also called expression-associated CpG loci, eCpG). However, no open-source tools are available to provide eQTM mapping. In addition, eQTM mapping can involve a large number of comparisons which may prevent the analyses due to limitations of computational resources. Here, we describe Torch-eCpG (tecpg), an open-source tool developed in Python to perform eQTM mapping that includes an optimized implementation that can use the graphical processing unit (GPU) to reduce runtime.
Files
Torch-eCpG - a fast and scalable eQTM mapper GPU CIBB 2025.pdf
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Additional details
Related works
- Is described by
- Journal article: 10.1186/s12859-024-05670-4 (DOI)
Funding
- National Cancer Institute
- An Investigation of the Molecular Mechanisms for and Prediction of the Severity of Cancer Chemotherapy-Related Fatigue Using a Multi-staged Integrated Omics Approach CA233774
Software
- Repository URL
- https://github.com/kordk/torch-ecpg
- Programming language
- Python, Cuda
- Development Status
- Active