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