Introduction | How to run Clomial? | Reference
Package: Clomial 1.49.0
Habil Zare
Clomial: Infers clonal composition of a tumor
Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.
Authors:
Clomial_1.49.0.tar.gz
Clomial_1.49.0.zip(r-4.7)Clomial_1.49.0.zip(r-4.6)Clomial_1.49.0.zip(r-4.5)
Clomial_1.49.0.tgz(r-4.6-any)Clomial_1.49.0.tgz(r-4.5-any)
Clomial_1.49.0.tar.gz(r-4.7-any)Clomial_1.49.0.tar.gz(r-4.6-any)
Clomial_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Clomial/json (API)
| # Install 'Clomial' in R: |
| install.packages('Clomial', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- breastCancer - Breast cancer data for clonal decomposition.
- Clomial1000 - Pre-computed results of Clomial.
On BioConductor:Clomial-1.49.0(bioc 3.24)Clomial-1.48.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneticsgeneticvariabilitysequencingclusteringmultiplecomparisonbayesiandnaseqexomeseqtargetedresequencingimmunooncology
Last updated from:ca3ec4d09c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 134 | ||
| linux-devel-x86_64 | NOTE | 212 | ||
| source / vignettes | OK | 156 | ||
| linux-release-x86_64 | NOTE | 163 | ||
| macos-release-arm64 | NOTE | 111 | ||
| macos-oldrel-arm64 | NOTE | 114 | ||
| windows-devel | NOTE | 176 | ||
| windows-release | NOTE | 158 | ||
| windows-oldrel | NOTE | 158 | ||
| wasm-release | OK | 93 |
Exports:choose.bestClomialClomial.generate.dataClomial.iterateClomial.likelihoodcompute.biccompute.errors
Dependencies:matrixStatspermute
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fits a binomial model to data from multiple samples of a single tumor to infer its clonal decomposition. | Clomial-package |
| Breast cancer data for clonal decomposition. | breastCancer |
| Chooses the best trained Clomial model. | choose.best |
| Fits several binomial models to data from multiple samples of a single tumor. | Clomial |
| Generates simulated data to test performance of Clomial algorithm. | Clomial.generate.data |
| Runs EM iterations until convergence of the Clomial model. | Clomial.iterate |
| Computes the complete data log-likelihood of a Clomial model. | Clomial.likelihood |
| Pre-computed results of Clomial. | Clomial1000 |
| Computes BIC for a Clomial model. | compute.bic |
| Computes the error of a Clomial model. | compute.errors |