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miRSM

miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information

https://github.com/zhangjunpeng411/mirsm

Science Score: 26.0%

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    Low similarity (7.2%) to scientific vocabulary

Keywords

cerna mirna mirna-sponge mirna-targets modules

Keywords from Contributors

gene bioconductor-package genomics proteomics rna-seq differential-expression rna-seq-analysis derfinder rnaseq proteins
Last synced: 6 months ago · JSON representation

Repository

miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information

Basic Info
  • Host: GitHub
  • Owner: zhangjunpeng411
  • Language: HTML
  • Default Branch: devel
  • Homepage:
  • Size: 8 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 1
Topics
cerna mirna mirna-sponge mirna-targets modules
Created over 7 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog

README.md

miRSM R package

Introduction

This package provides several utility functions to study miRNA sponge or ceRNA 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.

Installation

{r echo=FALSE, results='hide', message=FALSE} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("miRSM")

A quick example to use miRSM package

```{r echo=FALSE, results='hide', message=FALSE}

Load miRSM package

suppressPackageStartupMessages(library(miRSM))

Load BRCA sample data

data(BRCASampleData)

Identifying gene co-expression modules using WGCNA

modulegenesWGCNA <- moduleWGCNA(ceRExp[, seqlen(150)], mRExp[, seqlen(150)])

Identifying miRNA sponge modules using sensitivity RV coefficient (SRVC)

miRSMWGCNASRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, modulegenesWGCNA, method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV")

Identifying sample-specific miRNA sponge modules

nsamples <- 3 modulegenesall <- moduleigraph(ceRExp[, 151:300], mRExp[, 151:300]) modulegenesexceptk <- lapply(seq(nsamples), function(i) moduleWGCNA(ceRExp[-i, seq(150)], mRExp[-i, seq(150)]))

miRSMSRVCall <- miRSM(miRExp, ceRExp[, 151:300], mRExp[, 151:300], miRTarget, modulegenesall, method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV") miRSMSRVCexceptk <- lapply(seq(nsamples), function(i) miRSM(miRExp[-i, ], ceRExp[-i, seq(150)], mRExp[-i, seq(150)], miRTarget, modulegenesexceptk[[i]], method = "SRVC", SMC.cutoff = 0.01, RVmethod = "RV"))

Modulegenesall <- miRSMSRVCall[[2]] Modulegenesexceptk <- lapply(seq(nsamples), function(i) miRSMSRVCexceptk[[i]][[2]])

ModulesSS <- miRSMSS(Modulegenesall, Modulegenesexceptk)

Functional analysis of miRNA sponge modules

miRSMWGCNASRVCgenes <- miRSMWGCNASRVC[[2]] miRSMWGCNASRVCFEA <- moduleFA(miRSMWGCNASRVCgenes, Analysis.type ="FEA") miRSMWGCNASRVCDEA <- moduleFA(miRSMWGCNASRVC_genes, Analysis.type = "DEA")

Cancer enrichment analysis of miRNA sponge modules

miRSM.CEA.pvalue <- moduleCEA(ceRExp, mRExp, BRCAgenes, miRSMWGCNASRVC_genes)

Validation of miRNA sponge interactions in miRNA sponge modules

Groundtruthcsv <- system.file("extdata", "Groundtruthhigh.csv", package="miRSM") Groundtruth <- read.csv(Groundtruthcsv, header=TRUE, sep=",") miRSM.Validate <- moduleValidate(miRSMWGCNASRVC_genes, Groundtruth)

Co-expression analysis of miRNA sponge modules

miRSMWGCNACoexpress <- moduleCoexpress(ceRExp, mRExp, miRSMWGCNASRVCgenes, resample = 10, method = "mean", test.method = "t.test")

Distribution analysis of sharing miRNAs

miRSMWGCNAsharemiRs <- sharemiRs(miRExp, miRTarget, miRSMWGCNASRVCgenes) miRSMWGCNAmiRdistribute <- modulemiRdistribute(miRSMWGCNAshare_miRs)

Predicting miRNA-target interactions

miRSMWGCNAmiRtarget <- modulemiRtarget(miRSMWGCNAsharemiRs, miRSMWGCNASRVC_genes)

Identifying miRNA sponge interactions

miRSMWGCNAmiRsponge <- modulemiRsponge(miRSMWGCNASRVCgenes)

```

License

GPL-3

Owner

  • Name: Junpeng Zhang
  • Login: zhangjunpeng411
  • Kind: user
  • Location: China
  • Company: Dali University

A teacher from Dali University. My research interests include Data Mining and Bioinformatics.

GitHub Events

Total
  • Push event: 4
  • Create event: 1
Last Year
  • Push event: 4
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 65
  • Total Committers: 5
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.246
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Junpeng Zhang z****1@y****m 49
Nitesh Turaga n****a@g****m 12
vobencha v****a@g****m 2
Hervé Pagès h****b@g****m 1
Hervé Pagès h****s@f****g 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 1 day
  • Average time to close pull requests: 2 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jamesbangbang1126 (1)
Pull Request Authors
  • zhangjunpeng411 (2)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 10,557 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: miRSM

Inferring miRNA sponge modules in heterogeneous data

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 10,557 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 15.3%
Stargazers count: 19.5%
Average: 21.3%
Downloads: 71.6%
Maintainers (1)
zjp@dali.edu.cn
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • BiBitR * imports
  • BicARE * imports
  • Biobase * imports
  • GFA * imports
  • GSEABase * imports
  • MCL * imports
  • MatrixCorrelation * imports
  • NMF * imports
  • PMA * imports
  • Rcpp * imports
  • SOMbrero * imports
  • SummarizedExperiment * imports
  • WGCNA * imports
  • biclust * imports
  • dbscan * imports
  • dynamicTreeCut * imports
  • energy * imports
  • fabia * imports
  • flashClust * imports
  • iBBiG * imports
  • igraph * imports
  • isa2 * imports
  • linkcomm * imports
  • mclust * imports
  • miRspongeR * imports
  • org.Hs.eg.db * imports
  • ppclust * imports
  • rqubic * imports
  • s4vd * imports
  • stats * imports
  • subspace * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests