miRSM
This is the released version of miRSM; for the devel version, see miRSM.
Inferring miRNA sponge modules in heterogeneous data
Bioconductor version: Release (3.23)
The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.
Author: Junpeng Zhang [aut, cre]
Maintainer: Junpeng Zhang <zjp at dali.edu.cn>
citation("miRSM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miRSM")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("miRSM")| miRSM: inferring miRNA sponge modules in heterogeneous data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Clustering, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, Software |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, BicARE, isa2, methods, rJava, Biobase, PMA, stats, dbscan, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy |
| System Requirements | |
| URL | https://github.com/zhangjunpeng411/miRSM |
| Bug Reports | https://github.com/zhangjunpeng411/miRSM/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | miRSM_2.8.0.tar.gz |
| Windows Binary (x86_64) | miRSM_2.8.0.zip |
| macOS Binary (big-sur-x86_64) | miRSM_2.8.0.tgz |
| macOS Binary (sonoma-arm64) | miRSM_2.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/miRSM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/miRSM |
| Bioc Package Browser | https://code.bioconductor.org/browse/miRSM/ |
| Package Short Url | https://bioconductor.org/packages/miRSM/ |
| Package Downloads Report | Download Stats |