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-4.5)SITH_1.1.0.zip(r-4.4)SITH_1.1.0.zip(r-4.3)
SITH_1.1.0.tgz(r-4.4-x86_64)SITH_1.1.0.tgz(r-4.4-arm64)SITH_1.1.0.tgz(r-4.3-x86_64)SITH_1.1.0.tgz(r-4.3-arm64)
SITH_1.1.0.tar.gz(r-4.5-noble)SITH_1.1.0.tar.gz(r-4.4-noble)
SITH_1.1.0.tgz(r-4.4-emscripten)SITH_1.1.0.tgz(r-4.3-emscripten)
SITH.pdf |SITH.html✨
SITH/json (API)
NEWS
| # 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-simulation
Last updated 6 months agofrom:ac69cfbbd3. Checks:ERROR: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Aug 30 2024 |
| R-4.5-win-x86_64 | ERROR | Aug 30 2024 |
| R-4.5-linux-x86_64 | ERROR | Aug 30 2024 |
| R-4.4-win-x86_64 | ERROR | Aug 30 2024 |
| R-4.4-mac-x86_64 | ERROR | Aug 30 2024 |
| R-4.4-mac-aarch64 | ERROR | Aug 30 2024 |
| R-4.3-win-x86_64 | ERROR | Aug 30 2024 |
| R-4.3-mac-x86_64 | ERROR | Aug 30 2024 |
| R-4.3-mac-aarch64 | ERROR | Aug 30 2024 |
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 |
