ssMutPA: Single-Sample Mutation-Based Pathway Analysis

A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.

Version: 0.1.0
Depends: R (≥ 3.5.0)
Imports: ggplot2, ggridges, grDevices, igraph, kernlab, maftools, Matrix, NbClust, parallel, pheatmap, RColorBrewer, stats, survival, utils
Suggests: knitr, qpdf, rmarkdown
Published: 2024-04-16
DOI: NA
Author: Junwei Han [aut, cre, cph], Yalan He [aut], Qian Wang [aut]
Maintainer: Junwei Han <hanjunwei1981 at 163.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: ssMutPA results

Documentation:

Reference manual: ssMutPA.pdf
Vignettes: ssMutPA

Downloads:

Package source: ssMutPA_0.1.0.tar.gz
Windows binaries: r-devel: ssMutPA_0.1.0.zip, r-release: ssMutPA_0.1.0.zip, r-oldrel: ssMutPA_0.1.0.zip
macOS binaries: r-release (arm64): ssMutPA_0.1.0.tgz, r-oldrel (arm64): ssMutPA_0.1.0.tgz, r-release (x86_64): ssMutPA_0.1.0.tgz, r-oldrel (x86_64): ssMutPA_0.1.0.tgz

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