Package: SITH 1.1.0
SITH: A Spatial Model of Intra-Tumor Heterogeneity
Implements a three-dimensional stochastic model of cancer growth and mutation similar to the one described in Waclaw et al. (2015) <doi:10.1038/nature14971>. Allows for interactive 3D visualizations of the simulated tumor. Provides a comprehensive summary of the spatial distribution of mutants within the tumor. Contains functions which create synthetic sequencing datasets from the generated tumor.
Authors:
SITH_1.1.0.tar.gz
SITH_1.1.0.zip(r-4.7-x86_64)SITH_1.1.0.zip(r-4.7-arm64)SITH_1.1.0.zip(r-4.6-x86_64)SITH_1.1.0.zip(r-4.6-arm64)SITH_1.1.0.zip(r-4.5-x86_64)
SITH_1.1.0.tgz(r-4.6-x86_64)SITH_1.1.0.tgz(r-4.6-arm64)SITH_1.1.0.tgz(r-4.5-x86_64)SITH_1.1.0.tgz(r-4.5-arm64)
SITH_1.1.0.tar.gz(r-4.7-arm64)SITH_1.1.0.tar.gz(r-4.7-x86_64)SITH_1.1.0.tar.gz(r-4.6-arm64)SITH_1.1.0.tar.gz(r-4.6-x86_64)
SITH_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SITH/json (API)
| # Install 'SITH' in R: |
| install.packages('SITH', repos = c('https://phillipnicol.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/phillipnicol/sith/issues
cancer-researchcancer-simulationcpp
Last updated from:ac69cfbbd3. Checks:14 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | ERROR | 104 | ||
| linux-devel-x86_64 | ERROR | 121 | ||
| source / vignettes | ERROR | 205 | ||
| linux-release-arm64 | ERROR | 142 | ||
| linux-release-x86_64 | ERROR | 121 | ||
| macos-release-arm64 | ERROR | 134 | ||
| macos-release-x86_64 | ERROR | 216 | ||
| macos-oldrel-arm64 | ERROR | 168 | ||
| macos-oldrel-x86_64 | ERROR | 267 | ||
| windows-devel-arm64 | ERROR | 324 | ||
| windows-devel-x86_64 | ERROR | 143 | ||
| windows-release-arm64 | ERROR | 322 | ||
| windows-release-x86_64 | ERROR | 78 | ||
| windows-oldrel-x86_64 | ERROR | 98 | ||
| wasm-release | OK | 107 |
Exports:bulkSampleplotSliceprogressionChainprogressionDAG_from_igraphrandomBulkSamplesrandomNeedlesrandomSingleCellssimulateTumorsingleCellspatialDistributionvisualizeTumor
Dependencies:Rcppscatterplot3d
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Visualize and analyze intratumor heterogeneity using a spatial model of tumor growth | SITH-package SITH |
| Simulate bulk sampling | bulkSample |
| 2D cross section of the simulated tumor | plotSlice |
| Create a linear chain graph to describe the order of mutations | progressionChain |
| Define the progression of mutations from an 'igraph' object | progressionDAG_from_igraph |
| Simulate multi-region bulk sampling | randomBulkSamples |
| Simulate fine needle aspiration | randomNeedles |
| Simulate single cell sequencing data | randomSingleCells |
| Spatial simulation of tumor growth | simulateTumor |
| Simulate single cell sequencing data | singleCell |
| Quantify the spatial distribution of mutants | spatialDistribution |
| Interactive visualization of the simulated tumor | visualizeTumor |