miRspongeR

The software tool "miRspongeR" addresses the complexity of microRNA (miRNA) sponges, RNA molecules with multiple tandem miRNA response elements that sequester miRNAs from their target mRNAs. Despite the increasing recognition of miRNA sponge importance, understanding their functions still needs to be improved still needs to be improved. miRspongeR, an R package, simplifies identifying and analyzing miRNA sponge interaction networks and modules. It includes seven popular methods and an integrative method for identifying miRNA sponge interactions. The package supports the validation of miRNA sponge interactions, identification of miRNA sponge modules, and functional enrichment and survival analysis of these modules.

Topic

Functional, regulatory and non-coding RNA;Microarray experiment;Molecular interactions, pathways and networks

Detail

  • Operation: microRNA detection;Enrichment analysis;miRNA expression analysis

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 2.6.0

  • Credit: The National Natural Science Foundation of China , the Applied Basic Research Foundation of Science and Technology of Yunnan Province, NHMRC Grant, the Australian Research Council Discovery Grant, the Presidential Foundation of Hefei Institutes of Physical Science, Chinese Academy of Sciences.

  • Input: -

  • Output: -

  • Contact: Junpeng Zhang zhangjunpeng411@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules.
  • Zhang J, et al. miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. 2019; 20:235. doi: 10.1186/s12859-019-2861-y
  • https://doi.org/10.1186/s12859-019-2861-y
  • PMID: 31077152
  • PMC: PMC6509829

Download and documentation

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