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 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")
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