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
README.md 0.2.9 Feb 22, 2018

README.md

RBiomirGS

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.

Installation:

  • Install devtools

    install.packages("devtools")
    
  • Install bioconductor

    source("https://bioconductor.org/biocLite.R")
    
    biocLite()
    
  • 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

0.2.6
  - rbiomirgs_histogram() changed to rbiomirgs_bar()
  - Bug fixes

0.2.5
  - p value thresholding added for rbiomirgs_histogram()
  - Bug fixes

0.2.4
  - miRNA and mRNA score output file name adjusted
  - Bug fixes

0.2.3
  - miRNA:mRNA interaction weight functionality fixed
  - Parameter optimization for rbiomirgs_logistic() adjusted
  - Other bug fixes


0.2.2 
  - arugment adjusted for the volcano plot function

0.2.1 
  - mRNA score output added

0.2.0
  - 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

0.1.8
  - 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

0.1.3
  - 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

0.1.2
  - 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

0.1.1
  - miRNA to mRNA function rbiomirGS_mrnalist() added.

0.1.0 
  - Initial release