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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "miRspongeR" in publications use:'
type: software
license: GPL-3.0-only
title: 'miRspongeR: Identification and analysis of miRNA sponge regulation'
version: 2.9.0
abstract: This package provides several functions to explore miRNA sponge (also called
  ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and
  transcriptomics data (including bulk, single-cell and spatial gene expression data).
  It provides eight popular methods for identifying miRNA sponge interactions, and
  an integrative method to integrate miRNA sponge interactions from different methods,
  as well as the functions to validate miRNA sponge interactions, and infer miRNA
  sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct
  survival analysis of miRNA sponge modules. By using a sample control variable strategy,
  it provides a function to infer sample-specific miRNA sponge interactions. In terms
  of sample-specific miRNA sponge interactions, it implements three similarity methods
  to construct sample-sample correlation network.
authors:
- family-names: Zhang
  given-names: Junpeng
  email: zhangjunpeng411@gmail.com
preferred-citation:
  type: article
  title: 'miRspongeR: an R/Bioconductor package for the identification and analysis
    of miRNA sponge interaction networks and modules'
  authors:
  - family-names: Zhang
    given-names: Junpeng
    email: zhangjunpeng411@gmail.com
  - family-names: Liu
    given-names: Lin
  - family-names: Xu
    given-names: Taosheng
  - family-names: Xie
    given-names: Yong
  - family-names: Zhao
    given-names: Chunwen
  - family-names: Li
    given-names: Jiuyong
  - family-names: Le
    given-names: Thuc Duy
  journal: BMC Bioinformatics
  year: '2019'
  volume: '20'
  url: https://doi.org/10.1186/s12859-019-2861-y
  start: '235'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/zhangjunpeng411/miRspongeR
url: https://github.com/zhangjunpeng411/miRspongeR
contact:
- family-names: Zhang
  given-names: Junpeng
  email: zhangjunpeng411@gmail.com
references:
- type: article
  title: 'miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation'
  authors:
  - family-names: Zhang
    given-names: Junpeng
  - family-names: Liu
    given-names: Lin
  - family-names: Zhang
    given-names: Wu
  - family-names: Li
    given-names: Xiaomei
  - family-names: Zhao
    given-names: Chunwen
  - family-names: Li
    given-names: Sijing
  - family-names: Li
    given-names: Jiuyong
  - family-names: Le
    given-names: Thuc Duy
  journal: Bioinformatics Advances
  year: '2022'
  volume: '2'
  issue: '1'
  url: https://doi.org/10.1093/bioadv/vbac063
  start: vbac063