Simple to use machine learning-based miRNA gene set analysis
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RBiomirGS 0.2.9 Feb 22, 2018
.DS_Store 0.2.6b Nov 22, 2017
.gitignore 0.2.6b Nov 22, 2017
LICENSE 0.2.6b Nov 22, 2017 0.2.9 Feb 22, 2018


Simple to use package for miRNA gene set analysis, with miRNA-mRNA interaction searching and human mRNA orthologs conversion functionalities.

To cite in publication

Zhang J, Storey KB. 2018. RBiomirGS: An all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration. PeerJ. 6: e4262.


  • Install devtools

  • Install bioconductor

  • Install stable release

    devtools::install_github("jzhangc/git_RBiomiRGS/RBiomirGS", repos = BiocInstaller::biocinstallRepos())
  • Install development build

    devtools::install_github("jzhangc/git_RBiomiRGS/RBiomirGS", repos = BiocInstaller::biocinstallRepos(), ref = "beta")

Update log

0.2.9 (Feb.22.2018)
  - ratioFC arugment added to rbiomirgs_logistic()
  - The default value for var_mirnaFC of rbiomirgs_logistic() changed to "logFC"

0.2.7 - 0.2.8
  - Citation information added
  - Bug fixes

  - rbiomirgs_histogram() changed to rbiomirgs_bar()
  - Bug fixes

  - p value thresholding added for rbiomirgs_histogram()
  - Bug fixes

  - miRNA and mRNA score output file name adjusted
  - Bug fixes

  - miRNA:mRNA interaction weight functionality fixed
  - Parameter optimization for rbiomirgs_logistic() adjusted
  - Other bug fixes

  - arugment adjusted for the volcano plot function

  - mRNA score output added

  - Package name changed to RBiomirGS
  - Plot functions added: rbiomirgs_volcano(), rbiomirgs_histogram()
  - Adjustments on the variable names for logitstic regression resutls
  - mRNA scoring modified with reversed sign, so that positive value means actiation and negative means inhibition. Same goes with the parameters obtained from logistic regression
  - Function names are now all lower cases
  - Bug fixes

  - Preparation for the plotting module
  - Description file updated
  - zzz.R file added
  - Bug fixes

0.1.6 - 0.1.7
  - Bug fixes

0.1.4 - 0.1.5 
  - logistic regression-based miRNA gene set analysis function rbiomirGS_logistic() added, featuring multiple parameter optimization algorithms as well as parallel computing
  - many "quality of life" features added for both rbiomirGS_logistic() and rbiomirGS_mrnalist() function
  - codes optmized to reduce redundancy 
  - Bug fixes

  - rbiomirGS_mrnalist() now is able to connect to ensembl database to convert mmu/rno entrez gene IDs to the hsa ortholog entrez IDs
  - rbiomirGS_gmt() function added to load gmt gene set files from ensembl databases
  - Bug fixes

  - In addition to the environment, rbiomirGS_mrnalist() now outputs csv files of the mRNA resutls, as well as a hsa entrez list to the environment for modelling use

  - miRNA to mRNA function rbiomirGS_mrnalist() added.

  - Initial release