OmicsARules

OmicsARules is an R package for identifying and analyzing co-occurring gene alterations within single or multiple omics datasets. It utilizes association rule mining, a data mining technique, to discover patterns of concerted changes among genes across different regulation levels, such as DNA methylation and RNA-seq data.

Key features of OmicsARules:

1. Lamda3: A novel rule-interestingness measure embedded in OmicsARules to evaluate and prioritize the most biologically meaningful gene associations. Lamda3 has demonstrated better performance in capturing biological significance than other rule-ranking measures.

2. Multi-omics analysis: OmicsARules can illustrate the mechanistic connections between different omics levels, such as DNA methylation and transcription, by analyzing combined omics datasets.

3. Frequent pattern mining: The package searches for concurrent patterns among frequently altered genes, providing a new perspective for exploring single or multiple omics data across sequencing platforms.

Topic

RNA-Seq;Proteomics;Epigenetics;Gene expression;Gene transcripts

Detail

  • Operation: Data retrieval;Visualisation;Expression analysis

  • Software interface: Library

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Natural Science Foundation of China.

  • Input: -

  • Output: -

  • Contact: Jianzhen Xu jzxu01@stu.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • OmicsARules: a R package for integration of multi-omics datasets via association rules mining.
  • Chen D, et al. OmicsARules: a R package for integration of multi-omics datasets via association rules mining. OmicsARules: a R package for integration of multi-omics datasets via association rules mining. 2019; 20:554. doi: 10.1186/s12859-019-3171-0
  • https://doi.org/10.1186/S12859-019-3171-0
  • PMID: 31703610
  • PMC: PMC6839229

Download and documentation

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