Package: ssMutPA
Type: Package
Title: Single-Sample Mutation-Based Pathway Analysis
Version: 0.1.1
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
Config/pak/sysreqs: libglpk-dev libbz2-dev liblzma-dev libxml2-dev
        xz-utils zlib1g-dev
Repository: https://hanjunwei-lab.r-universe.dev
Date/Publication: 2024-10-16 11:53:57 UTC
RemoteUrl: https://github.com/hanjunwei-lab/ssmutpa
RemoteRef: HEAD
RemoteSha: 9aecd48dd6cdce7a24ad07b8a44978f9275d34df
NeedsCompilation: no
Packaged: 2026-06-08 09:15:46 UTC; root
Author: Junwei Han [aut, cre, cph],
  Yalan He [aut],
  Qian Wang [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>