Package: miRSM 2.9.0

Junpeng Zhang

miRSM: Inferring miRNA sponge modules in heterogeneous data

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.

Authors:Junpeng Zhang [aut, cre]

miRSM_2.9.0.tar.gz
miRSM_2.9.0.zip(r-4.7)miRSM_2.9.0.zip(r-4.6)miRSM_2.9.0.zip(r-4.5)
miRSM_2.9.0.tgz(r-4.6-x86_64)miRSM_2.9.0.tgz(r-4.6-arm64)miRSM_2.9.0.tgz(r-4.5-x86_64)miRSM_2.9.0.tgz(r-4.5-arm64)
miRSM_2.9.0.tar.gz(r-4.7-arm64)miRSM_2.9.0.tar.gz(r-4.7-x86_64)miRSM_2.9.0.tar.gz(r-4.6-arm64)miRSM_2.9.0.tar.gz(r-4.6-x86_64)
miRSM_2.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
miRSM/json (API)

# Install 'miRSM' in R:

install.packages('miRSM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhangjunpeng411/mirsm/issues

Uses libs:

c++– GNU Standard C++ Library v3
openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

BRCA_genes - BRCA genes
ceRExp - CeRNA expression data
miRExp - MiRNA expression data
miRTarget - MiRNA-target ineractions
mRExp - MRNA expression data

On BioConductor:miRSM-2.9.0(bioc 3.24)miRSM-2.8.0(bioc 3.23)

geneexpression biomedicalinformatics clustering genesetenrichment microarray software generegulation genetarget cerna mirna mirna-sponge mirna-targets modules cpp openjdk

5.30 score 5 stars 5 scripts 1 mentions 20 exports 228 dependencies

Last updated from:82a1c3b2a7. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	369
linux-devel-arm64	NOTE	487
linux-devel-x86_64	NOTE	606
source / vignettes	OK	551
linux-release-arm64	NOTE	556
linux-release-x86_64	NOTE	642
macos-release-arm64	NOTE	280
macos-release-x86_64	NOTE	652
macos-oldrel-arm64	NOTE	365
macos-oldrel-x86_64	NOTE	789
windows-devel	NOTE	500
windows-release	NOTE	517
windows-oldrel	NOTE	493
wasm-release	OK	307

Exports:cor_binary diff_module miRSM miRSM_SS module_biclust module_CEA module_clust module_Coexpress module_FA module_GFA module_group_sim module_igraph module_miRdistribute module_miRsponge module_miRtarget module_NMF module_ProNet module_Validate module_WGCNA share_miRs

Dependencies:abind aisdk annotate AnnotationDbi ape aplot askpass backports base64enc BicARE Biobase BiocGenerics BiocManager Biostrings bit bit64 blob boot bslib cachem callr checkmate class classInt cli cluster clusterProfiler codetools colorspace commonmark cpp11 crayon curl data.table DBI dbscan DelayedArray deldir digest dir.expiry doParallel DOSE dplyr dynamicTreeCut e1071 energy enrichit enrichplot evaluate expm fabia farver fastcluster fastmap filelock flashClust fontawesome fontBitstreamVera fontLiberation fontquiver foreach foreign Formula formula.tools fs gdtools generics GenomicRanges GFA ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree ggwordcloud glue GO.db GOSemSim graph graphite graphlayouts gridBase gridExtra gridGraphics gridtext GSEABase gsl gson gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 igraph impute inaparc interp IRanges isa2 isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr kpeaks labeling later lattice lazyeval lhs lifecycle litedown lubridate magrittr markdown MASS Matrix MatrixCorrelation MatrixGenerics matrixStats MCL mclust memoise metR mime multtest nlme NMF nnet openssl operator.tools org.Hs.eg.db otel patchwork pillar pkgconfig plotrix plyr PMA png polyclip ppclust pracma preprocessCore prettyunits processx progress promises proxy ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db ReactomePA registry reshape2 rJava rlang rmarkdown rngtools rpart RSpectra RSQLite rstudioapi s2 S4Arrays S4Vectors S7 sass scales scatterpie scatterplot3d Seqinfo sf shiny SOMbrero sourcetools SparseArray stringi stringr SummarizedExperiment survival sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree timechange tinytex treeio tweenr units utf8 vctrs viridis viridisLite WGCNA withr wk xfun XML xml2 xtable XVector yaml yulab.utils

miRSM: inferring miRNA sponge modules in heterogeneous data

Rendered frommiRSM.Rmdusingknitr::rmarkdown

Last update: 2026-01-15
Started: 2018-08-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BRCA genes	BRCA_genes
ceRNA expression data	ceRExp
cor_binary	cor_binary
diff_module	diff_module
miRNA expression data	miRExp
miRSM	miRSM
miRSM_SS	miRSM_SS
miRNA-target ineractions	miRTarget
module_biclust	module_biclust
module_CEA	module_CEA
module_clust	module_clust
module_Coexpress	module_Coexpress
module_FA	module_FA
module_GFA	module_GFA
module_group_sim	module_group_sim
module_igraph	module_igraph
module_miRdistribute	module_miRdistribute
module_miRsponge	module_miRsponge
module_miRtarget	module_miRtarget
module_NMF	module_NMF
module_ProNet	module_ProNet
module_Validate	module_Validate
module_WGCNA	module_WGCNA
mRNA expression data	mRExp
share_miRs	share_miRs