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:Kevin R. Coombes, Mark Zucker

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'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/oompa

11 exports 0.00 score 89 dependencies

Last updated 2 years agofrom:10e984dc8d5c6d54f12db9ab583ff73f15029b6a

Exports:dataGengenerateSimplexgenerateTumorDatagetCloneplotTumorDatarunAlgsampleSimplexseekClonesTumortumorGenWeightVector

Dependencies:abindbackportsbootbriobroomcallrcarcarDataclicolorspacecombinatcorrplotcowplotcpp11crayoncurldescdiffobjdigestdplyrevaluatefansifarverfsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmc2dmgcvminqamunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgbuildpkgconfigpkgloadpolynompraiseprocessxpspurrrquantmodquantregR6RColorBrewerRcppRcppEigenrematch2rlangrprojrootrstatixscalesSparseMstringistringrsurvivaltestthattibbletidyrtidyselectTTRutf8vctrsviridisLitewaldowithrxtszoo

CloneSeeker

Rendered fromCloneSeeker.Rnwusingutils::Sweaveon May 22 2024.

Last update: 2019-04-12
Started: 2019-04-12

Readme and manuals

Help Manual

Help pageTopics
Seeking Tumor Clones From DatarunAlg seekClones
Simplices and Clonal FractionsgenerateSimplex sampleSimplex Simplices
Simulating Tumor ClonesdataGen 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