The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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.

Version: 1.1
Depends: R (≥ 3.2.1), igraph
Imports: stats, graphics, utils, grDevices
Suggests: Matrix, graph
Published: 2018-09-26
DOI: 10.32614/CRAN.package.LncPath
Author: Junwei Han, Zeguo Sun
Maintainer: Junwei Han <hanjunwei1981 at 163.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: LncPath results

Documentation:

Reference manual: LncPath.pdf
Vignettes: LncPath Overview

Downloads:

Package source: LncPath_1.1.tar.gz
Windows binaries: r-devel: LncPath_1.1.zip, r-release: LncPath_1.1.zip, r-oldrel: LncPath_1.1.zip
macOS binaries: r-release (arm64): LncPath_1.1.tgz, r-oldrel (arm64): LncPath_1.1.tgz, r-release (x86_64): LncPath_1.1.tgz, r-oldrel (x86_64): LncPath_1.1.tgz
Old sources: LncPath archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=LncPath to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.