Package: LncPath 1.1
LncPath: Identifying the Pathways Regulated by LncRNA Sets of Interest
Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.
Authors:
LncPath_1.1.tar.gz
LncPath_1.1.zip(r-4.5)LncPath_1.1.zip(r-4.4)LncPath_1.1.zip(r-4.3)
LncPath_1.1.tgz(r-4.4-any)LncPath_1.1.tgz(r-4.3-any)
LncPath_1.1.tar.gz(r-4.5-noble)LncPath_1.1.tar.gz(r-4.4-noble)
LncPath_1.1.tgz(r-4.4-emscripten)LncPath_1.1.tgz(r-4.3-emscripten)
LncPath.pdf |LncPath.html✨
LncPath/json (API)
| # Install 'LncPath' in R: |
| install.packages('LncPath', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hanjunwei-lab/lncpath/issues
- LncPathEnvir - The variables in the environment variable 'LncPathEnvir' of the system
Last updated 4 years agofrom:bf44cfe115. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 06 2024 |
| R-4.5-win | NOTE | Nov 06 2024 |
| R-4.5-linux | NOTE | Nov 06 2024 |
| R-4.4-win | NOTE | Nov 06 2024 |
| R-4.4-mac | NOTE | Nov 06 2024 |
| R-4.3-win | NOTE | Nov 06 2024 |
| R-4.3-mac | NOTE | Nov 06 2024 |
Exports:calFDcalTdrawAHeatMapESNormfindSigGenesgeneSetDetailgetExampleDatagetNetinitializeLncPathEnvirlncPathlncPath.EnrichmentScorelncPath.EnrichmentScore2lncPath.HeatMapPlotlncPath2TableplotRunningESprintSignifResultRandomWalk2igraphrw
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Draw a heatmap for the genes of a pathway | drawAHeatMap |
| Find genes significantly differentially expressed between two conditions. | findSigGenes |
| Gain insight into the detail of the genes in a certain pathway | geneSetDetail |
| Get the example data | getExampleData |
| Get the background lncRNA-mRNA interaction network | getNet |
| Identify pathways synergisticly regulated by lncRNA sets. | lncPath |
| Simplify the lncPath object into table | lncPath2Table |
| The variables in the environment variable 'LncPathEnvir' of the system | LncPathEnvir |
| Visualize the Kolmogorov-Smirnov running score of pathway | plotRunningES |
| Output the details of significant pathways | printSignifResult |
