Introduction | MAF field requirements | Installation | Overview of the package | Obtain the gene mutation status matrix | Calculate the single-sample mutation-based pathway enrichment score. | Identification of cancer subtypes based on unsupervised spectral clustering algorithm. | Visualization results
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:
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✨
DESCRIPTION
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
Last updated from:9aecd48dd6. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 188 | ||
| source / vignettes | OK | 242 | ||
| linux-release-x86_64 | OK | 173 | ||
| macos-release-arm64 | OK | 173 | ||
| macos-oldrel-arm64 | OK | 145 | ||
| windows-devel | OK | 117 | ||
| windows-release | OK | 124 | ||
| windows-oldrel | OK | 150 | ||
| wasm-release | OK | 118 |
Exports:dotplotFastSEAscoreget_heatmapget_indicateget_mut_statusget_RWR_ESget_samp_classget_seeds_scoreget_univarCox_resultmountain_plotMRWROncoplot
Dependencies:clicpp11data.tableDNAcopyfarverggplot2ggridgesgluegtableigraphisobandkernlablabelinglatticelifecyclemaftoolsmagrittrMatrixNbClustpheatmappkgconfigR6RColorBrewerRhtslibrlangS7scalessurvivalvctrsviridisLitewithr
