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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

    if (!requireNamespace("BiocManager"))
        install.packages("BiocManager")
        
    BiocManager::install()
    
  • Install stable release

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

    devtools::install_github("jzhangc/git_RBiomiRGS/RBiomirGS", repos = BiocManager::repositories(), ref = "beta")
    

Update log

0.2.21 (May.20.2024)
  - Plotting functionalities have updated with the ggplot2 >= 3.5.0 compatibility
    - Due to the ggplot2 (>=3.5.0) native support for axis duplication, the custome script for the functionality is no longer needed
    - The package updated with ggplot2 (>=3.5.0) dependency

0.2.20 (January.3.2024)
  - The hsa_entrez list now is also a "mir_entrez_list" class
  - rbiomirgs_logistic and rbiomirgs_logisticV2 updated with argument check

0.2.19 (September.6.2023)
  - A bug fixed for rbiomirgs_volcano() where the function will crash when no FDR significance was found while FDR correction is active

0.2.18 (March.25.2023)
  - A bug fixed for rbiomirgs_logistic() where the "mir_entrez_list" check fails to give proper error messages

0.2.17 (November.16.2022)
  - rbiomirgs_logistic() updated with error message ("incompabile") if to use a "mir_entrez_list" class

0.2.16 (March.21.2022)
  - It is now possible to custom file name for rbiomirgs_volcano() and rbiomirgs_bar()
  - A bug fixed for rbiomirgs_volcano() where label for target passing alpha wasn't properly displayed when fdr=TRUE

0.2.15 (December.20.2021)
  - The entrez list derived from mirnascan() now has both "list" and "mir_entrez_list" classes
  - A new rbiomirgs_logisticV2() function added that always checks if the "mrnalist" is a "mir_entrez_list" class
    - The original rbiomirgs_logistic() function still available for compatibility purposes
    - The new "mir_entrez_list" classes works with both rbiomirgs_logistic and rbiomirgs_logisticV2() functions
    - The old entrez list (i.e. only a "list" class) will NOT work with the rbiomirgs_logisticV2() function
    
0.2.14 (April.16.2021)
  - p_line_offset added to the rbiomirgs_volcano() function. See manual for details

0.2.13 (Mar.25.2021)
  - rbiomirgs_logistic() updated to handle empty miRNA ID entries
    - Small updates to rbiomirgs_logistic() message delivery

0.2.12 (Aug.12.2019)
  - The default server url updated to "http://multimir.org/cgi-bin/multimir_univ.pl"
  - rbiomirgs_mrnascan() updated with updated biomaRt entrezgene identifier
  - Small fixes

0.2.10
  - Additional argument check added to rbiomirgs_mrnascan()
  - New bioconductor installation instructions added

0.2.9
  - 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

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