Package: ssMutPA
Type: Package
Title: Single-Sample Mutation-Based Pathway Analysis
Version: 0.1.2
Authors@R: c(person(given = "Junwei", family = "Han", email = "hanjunwei1981@163.com", role  = c("aut", "cre", "cph")),
             person(given = "Yalan", family = "He", role  = "aut"),
             person(given = "Qian", family = "Wang", role  = "aut"))
Description: 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.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Imports: ggplot2, ggridges, grDevices, igraph, kernlab, maftools,
        Matrix, NbClust, parallel, pheatmap, RColorBrewer, stats,
        survival, utils
Suggests: knitr, qpdf, rmarkdown
Depends: R (>= 4.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-10-15 12:34:47 UTC; DELL
Author: Junwei Han [aut, cre, cph],
  Yalan He [aut],
  Qian Wang [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Repository: CRAN
Date/Publication: 2024-10-15 22:00:02 UTC
Built: R 4.4.3; ; 2025-12-05 04:14:52 UTC; windows
