Package: ssMutPA 0.1.0

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_0.1.0.tar.gz
ssMutPA_0.1.0.zip(r-4.5)ssMutPA_0.1.0.zip(r-4.4)ssMutPA_0.1.0.zip(r-4.3)
ssMutPA_0.1.0.tgz(r-4.4-any)ssMutPA_0.1.0.tgz(r-4.3-any)
ssMutPA_0.1.0.tar.gz(r-4.5-noble)ssMutPA_0.1.0.tar.gz(r-4.4-noble)
ssMutPA_0.1.0.tgz(r-4.4-emscripten)ssMutPA_0.1.0.tgz(r-4.3-emscripten)
ssMutPA.pdf |ssMutPA.html✨
ssMutPA/json (API)

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

Peer review:

Datasets:
  • 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.
  • Seeds_Score - Seeds_Score The local weight of seed nodes.
  • 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.
  • samp_class_onco - Samp_class_onco
  • sample_class - Sample_class The subtype labels of samples.
  • sur_onco - Sur_onco

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

12 exports 0.09 score 40 dependencies 187 downloads

Last updated 5 months agofrom:4a71f50ded. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winOKSep 14 2024
R-4.5-linuxOKSep 14 2024
R-4.4-winOKSep 14 2024
R-4.4-macOKSep 14 2024
R-4.3-winOKSep 14 2024
R-4.3-macOKSep 14 2024

Exports:dotplotFastSEAscoreget_heatmapget_indicateget_mut_statusget_RWR_ESget_samp_classget_seeds_scoreget_univarCox_resultmountain_plotMRWROncoplot

Dependencies:clicolorspacecpp11data.tableDNAcopyfansifarverggplot2ggridgesgluegtableigraphisobandkernlablabelinglatticelifecyclemaftoolsmagrittrMASSMatrixmgcvmunsellNbClustnlmepheatmappillarpkgconfigR6RColorBrewerRhtslibrlangscalessurvivaltibbleutf8vctrsviridisLitewithrzlibbioc

ssMutPA

Yalan He,Qian Wang,Junwei Han

Rendered fromssMutPA.Rmdusingknitr::knitron Sep 14 2024.

Last update: 2024-04-17
Started: 2024-04-17