Package: MiRSEA 1.1
MiRSEA: 'MicroRNA' Set Enrichment Analysis
The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.
Authors:
MiRSEA_1.1.tar.gz
MiRSEA_1.1.zip(r-4.5)MiRSEA_1.1.zip(r-4.4)MiRSEA_1.1.zip(r-4.3)
MiRSEA_1.1.tgz(r-4.4-any)MiRSEA_1.1.tgz(r-4.3-any)
MiRSEA_1.1.tar.gz(r-4.5-noble)MiRSEA_1.1.tar.gz(r-4.4-noble)
MiRSEA_1.1.tgz(r-4.4-emscripten)MiRSEA_1.1.tgz(r-4.3-emscripten)
MiRSEA.pdf |MiRSEA.html✨
MiRSEA/json (API)
| # Install 'MiRSEA' in R: |
| install.packages('MiRSEA', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hanjunwei-lab/mirsea/issues
- envData - The variables in the environment include predefine pathway, target information of miRNAs,an expression profile and a example result of miRNA list
statisticspathwaysmicrornaenrichment analysis
Last updated 4 years agofrom:2914d2e41b. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 10 2024 |
| R-4.5-win | NOTE | Nov 10 2024 |
| R-4.5-linux | NOTE | Nov 10 2024 |
| R-4.4-win | NOTE | Nov 10 2024 |
| R-4.4-mac | NOTE | Nov 10 2024 |
| R-4.3-win | NOTE | Nov 10 2024 |
| R-4.3-mac | NOTE | Nov 10 2024 |
Exports:Corrp2miRfileEnrichmentScoreEnrichmentScore2GetenvirGetExampleDataGetMiRTargetDataGetPathwayDataHeatMapPlotinitializeMiRSEAMirSEAMsReportPlotCorrelationPlotHeatMapPlotRunEnrichmentS2N
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| MicroRNA Set Enrichment Analysis | MiRSEA-package MiRSEA |
| create a pathway-microRNA(miRNA) profile and a p value matrix | Corrp2miRfile |
| Computes the enrichment score | EnrichmentScore |
| Computes the enrichment score faster | EnrichmentScore2 |
| The variables in the environment include predefine pathway, target information of miRNAs,an expression profile and a example result of miRNA list | envData example.cls example.gct mfile miRList p p2miR pathway |
| Get the example data | GetExampleData |
| Get the data of microRNA(miRNA) and target genes | GetMiRTargetData |
| Get the gene sets of pathways | GetPathwayData |
| Plot a heatmap | HeatMapPlot |
| Identify dysregulated pathways based on microRNA (miRNA) set enrichment analysis | MirSEA |
| Produce report for a microRNA (abbreviated miRNA) set | MsReport |
| Plot global microRNA(miRNA) correlation profile | PlotCorrelation |
| Plot a heat map | PlotHeatMap |
| Plot running microRNAs(miRNAs) enrichment score | PlotRunEnrichment |
| calculate signal to noise ratio for microRNAs(miRNAs) | S2N |
