Package: CloneSeeker 1.0.11
Kevin R. Coombes
CloneSeeker: Seeking and Finding Clones in Copy Number and Sequencing Data
Defines the classes and functions used to simulate and to analyze data sets describing copy number variants and, optionally, sequencing mutations in order to detect clonal subsets. See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.
Authors:
CloneSeeker_1.0.11.tar.gz
CloneSeeker_1.0.11.tar.gz(r-4.5-noble)CloneSeeker_1.0.11.tar.gz(r-4.4-noble)
CloneSeeker_1.0.11.tgz(r-4.4-emscripten)CloneSeeker_1.0.11.tgz(r-4.3-emscripten)
CloneSeeker.pdf |CloneSeeker.html✨
CloneSeeker/json (API)
| # Install 'CloneSeeker' in R: |
| install.packages('CloneSeeker', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
Last updated 3 years agofrom:10e984dc8d. Checks:1 OK, 1 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 17 2025 |
| R-4.5-linux | NOTE | Feb 17 2025 |
Exports:dataGengenerateSimplexgenerateTumorDatagetCloneplotTumorDatarunAlgsampleSimplexseekClonesTumortumorGenWeightVector
Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecombinatcorrplotcowplotcpp11curlDerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmc2dmgcvmicrobenchmarkminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrquantmodquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectTTRutf8vctrsviridisLitewithrxtszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Seeking Tumor Clones From Data | runAlg seekClones |
| Simplices and Clonal Fractions | generateSimplex sampleSimplex Simplices |
| Simulating Tumor Clones | dataGen generateTumorData plotTumorData tumorGen |
| Class "Tumor" | coerce,Tumor,list-method getClone summary,Tumor-method Tumor Tumor-class |
| Class "WeightVector" | coerce,WeightVector,numeric-method WeightVector WeightVector-class |