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LncPath  

Identifying the Pathways Regulated by LncRNA Sets of Interest
View on CRAN: Click here


Download and install LncPath package within the R console
Install from CRAN:
install.packages("LncPath")

Install from Github:
library("remotes")
install_github("cran/LncPath")

Install by package version:
library("remotes")
install_version("LncPath", "1.1")



Attach the package and use:
library("LncPath")
Maintained by
Junwei Han
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-05-16
Latest Update: 2018-09-26
Description:
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.
How to cite:
Junwei Han (2016). LncPath: Identifying the Pathways Regulated by LncRNA Sets of Interest. R package version 1.1, https://cran.r-project.org/web/packages/LncPath. Accessed 09 Apr. 2025.
Previous versions and publish date:
1.0 (2016-05-16 14:45), 1.1 (2018-09-26 16:20)
Other packages that cited LncPath R package
View LncPath citation profile
Other R packages that LncPath depends, imports, suggests or enhances
Complete documentation for LncPath
Functions, R codes and Examples using the LncPath R package
Some associated functions: LncPath-internal . LncPathEnvir . drawAHeatMap . findSigGenes . geneSetDetail . getExampleData . getNet . lncPath . lncPath2Table . plotRunningES . printSignifResult . 
Some associated R codes: Full LncPath package functions and examples
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