Package: CeRNASeek 2.1.3
Mengying Zhang
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.
Authors:
CeRNASeek_2.1.3.tar.gz
CeRNASeek_2.1.3.tar.gz(r-4.5-noble)CeRNASeek_2.1.3.tar.gz(r-4.4-noble)
CeRNASeek_2.1.3.tgz(r-4.4-emscripten)CeRNASeek_2.1.3.tgz(r-4.3-emscripten)
CeRNASeek.pdf |CeRNASeek.html✨
CeRNASeek/json (API)
| # Install 'CeRNASeek' in R: |
| install.packages('CeRNASeek', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- dataset - Data for Examples
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
competing endogenous rna (cerna)geneexpressiontripletfunctionsoftware
Last updated 5 years agofrom:4a33060d7a. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-linux | OK | Nov 12 2024 |
Exports:ceRNA.appceRNA.basicceRNA.cerniaceRNA.cmiceRNA.corceRNA.enrichceRNA.NetceRNA.survsurv.plot
Dependencies:clicpp11gluegtoolsigraphlatticelifecyclemagrittrMatrixpkgconfigrlangsurvivalvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CeRNASeek | CeRNASeek-package CeRNASeek |
| identify the miRNAs that co-regulate the gene pairs of interest. | ceRNA.app |
| Identifying miRNA sponge interactions using ceRNA.basic function | ceRNA.basic |
| identifying miRNA sponge interactions using ceRNA.cernia function. | ceRNA.cernia |
| identifying miRNA sponge interactions using ceRNA.cmi function. | ceRNA.cmi |
| identifying miRNA sponge interactions using ceRNA.cor function | ceRNA.cor |
| Enrich the biological functions of interest. | ceRNA.enrich |
| visualize and analyze the identified ceRNA-ceRNA network using ceRNA.Net function | ceRNA.Net |
| survival analysis of ceRNA ternary relationship pairs | ceRNA.surv |
| Data for Examples | dataset |
| Draw survival curve | surv.plot |