Package: ssMutPA 0.1.1

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.

Authors:Junwei Han [aut, cre, cph], Yalan He [aut], Qian Wang [aut]

ssMutPA_0.1.1.tar.gz
ssMutPA_0.1.1.zip(r-4.7)ssMutPA_0.1.1.zip(r-4.6)ssMutPA_0.1.1.zip(r-4.5)
ssMutPA_0.1.1.tgz(r-4.6-any)ssMutPA_0.1.1.tgz(r-4.5-any)
ssMutPA_0.1.1.tar.gz(r-4.7-any)ssMutPA_0.1.1.tar.gz(r-4.6-any)
ssMutPA_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ssMutPA/json (API)

# Install 'ssMutPA' in R:
install.packages('ssMutPA', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hanjunwei-lab/ssmutpa/issues

Datasets:
  • cox_data - Cox_data Univariate cox proportional hazards regression data.
  • dot_data - Dot_data A data frame.
  • mut_onco - Mut_onco A binary mutation matrix.
  • mut_status - Mut_status A binary mutation matrix.
  • Path_ES - Path_ES Single-sample mutation-based pathway enrichment score profiles.
  • Path_Name - Path_Name
  • RWR_res - RWR_res Random walk results based on mutated genes in a single sample.
  • samp_class_onco - Samp_class_onco
  • sample_class - Sample_class The subtype labels of samples.
  • Seeds_Score - Seeds_Score The local weight of seed nodes.
  • sur_onco - Sur_onco

On CRAN:

Conda:

3.70 score 9 scripts 216 downloads 12 exports 31 dependencies

Last updated from:9aecd48dd6. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK173
source / vignettesOK256
linux-release-x86_64OK161
macos-release-arm64OK187
macos-oldrel-arm64OK154
windows-develOK123
windows-releaseOK118
windows-oldrelOK115
wasm-releaseOK132

Exports:dotplotFastSEAscoreget_heatmapget_indicateget_mut_statusget_RWR_ESget_samp_classget_seeds_scoreget_univarCox_resultmountain_plotMRWROncoplot

Dependencies:clicpp11data.tableDNAcopyfarverggplot2ggridgesgluegtableigraphisobandkernlablabelinglatticelifecyclemaftoolsmagrittrMatrixNbClustpheatmappkgconfigR6RColorBrewerRhtslibrlangS7scalessurvivalvctrsviridisLitewithr

ssMutPA

Yalan He,Qian Wang,Junwei Han

Rendered fromssMutPA.Rmdusingknitr::knitron May 09 2026.

Last update: 2024-10-10
Started: 2024-10-10