Package: miRSM 2.3.0

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_2.3.0.tar.gz
miRSM_2.3.0.zip(r-4.5)miRSM_2.3.0.zip(r-4.4)
miRSM_2.3.0.tgz(r-4.4-x86_64)miRSM_2.3.0.tgz(r-4.4-arm64)
miRSM_2.3.0.tar.gz(r-4.5-noble)miRSM_2.3.0.tar.gz(r-4.4-noble)
miRSM_2.3.0.tgz(r-4.4-emscripten)
miRSM.pdf |miRSM.html✨
miRSM/json (API)
NEWS

# 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:

openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

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

On BioConductor:miRSM-2.3.0(bioc 3.21)miRSM-2.2.0(bioc 3.20)

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

5.75 score 4 stars 5 scripts 167 downloads 1 mentions 20 exports 250 dependencies

Last updated 3 months agofrom:b0bce7fd9c. Checks:1 OK, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 19 2025
R-4.5-win-x86_64	NOTE	Jan 19 2025
R-4.5-linux-x86_64	NOTE	Jan 19 2025
R-4.4-win-x86_64	NOTE	Jan 19 2025
R-4.4-mac-x86_64	NOTE	Jan 19 2025
R-4.4-mac-aarch64	NOTE	Jan 19 2025

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 additivityTests ade4 annotate AnnotationDbi ape aplot askpass assertthat backports base64enc BH BiBitR BicARE biclust Biobase BiocGenerics BiocManager BiocParallel Biostrings bit bit64 blob boot bslib cachem checkmate class classInt cli cluster clusterProfiler codetools colorspace commonmark cowplot cpp11 crayon curl data.table DBI dbscan DelayedArray deldir dendextend digest doParallel DOSE dplyr dynamicTreeCut e1071 energy enrichplot evaluate expm fabia fansi farver fastcluster fastmap fastmatch fgsea flashClust flexclust fontawesome foreach foreign formatR Formula formula.tools fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GFA ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree ggvis ggwordcloud glue GO.db GOSemSim graph graphite graphlayouts gridBase gridExtra gridGraphics gridtext GSEABase gsl gson gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr iBBiG igraph impute inaparc interp IRanges irlba isa2 isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr kpeaks labeling lambda.r later lattice lazyeval lhs lifecycle linkcomm lubridate magrittr markdown MASS Matrix MatrixCorrelation MatrixGenerics matrixStats MCL mclust memoise metR mgcv mime modeltools multtest munsell nlme NMF nnet openssl operator.tools org.Hs.eg.db patchwork pillar pixmap pkgconfig plogr plotrix plyr PMA png polyclip ppclust pracma preprocessCore prettyunits progress promises proxy purrr qvalue R.methodsS3 R.oo R.utils R6 randomcoloR rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db ReactomePA registry reshape2 rJava rlang rmarkdown rngtools rpart rqubic RSpectra RSQLite rstudioapi Rtsne s2 S4Arrays s4vd S4Vectors sass scales scatterpie scatterplot3d sf shiny snow SOMbrero sourcetools sp SparseArray stringi stringr subspace SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect tidytree timechange tinytex treeio tweenr UCSC.utils units utf8 V8 vctrs viridis viridisLite WGCNA withr wk xfun XML xml2 xtable XVector yaml yulab.utils

miRSM: inferring miRNA sponge modules in heterogeneous data

Junpeng Zhang ([email protected]) School of Engineering, Dali University

Rendered frommiRSM.Rmdusingknitr::rmarkdownon Jan 19 2025.

Last update: 2024-04-05
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