R-universe search: cerna

Showing 7 of total 7 results (show query)

bioc

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.

Maintained by Junpeng Zhang. Last updated 5 months ago.

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

15.8 match 4 stars 5.68 score 5 scripts

bioc

ceRNAnetsim:Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

Maintained by Selcen Ari Yuka. Last updated 5 months ago.

networkinference systemsbiology network graphandnetwork transcriptomics cerna mirna network-biology network-simulator tcga tidygraph tidyverse

14.9 match 4 stars 5.76 score 12 scripts

bioc

SPONGE:Sparse Partial Correlations On Gene Expression

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Maintained by Markus List. Last updated 5 months ago.

geneexpression transcription generegulation networkinference transcriptomics systemsbiology regression randomforest machinelearning

14.0 match 5.36 score 38 scripts 1 dependents

bioc

miRspongeR:Identification and analysis of miRNA sponge regulation

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

Maintained by Junpeng Zhang. Last updated 5 months ago.

geneexpression biomedicalinformatics networkenrichment survival microarray software singlecell spatial rnaseq cerna mirna sponge

11.5 match 5 stars 5.88 score 8 scripts

cran

CeRNASeek:Identification and Analysis of ceRNA Regulation

Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.

Maintained by Mengying Zhang. Last updated 5 years ago.

competing endogenous rna (cerna)geneexpression triplet function software

40.2 match 1.00 score

shixinrui

SubpathwayLNCE:Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies.

Maintained by Xinrui Shi. Last updated 9 years ago.

statistics supathways lncrnas enrichment analysis cerna

13.8 match 2.00 score 2 scripts

bioc

GDCRNATools:GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.

Maintained by Ruidong Li. Last updated 5 months ago.

immunooncology geneexpression differentialexpression generegulation genetarget networkinference survival visualization genesetenrichment networkenrichment network rnaseq go kegg

4.1 match 5.64 score 44 scripts