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'))

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

2.00 score 8 scripts 220 downloads 11 exports 77 dependencies

Last updated 2 years agofrom:10e984dc8d. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024

Exports:dataGen generateSimplex generateTumorData getClone plotTumorData runAlg sampleSimplex seekClones Tumor tumorGen WeightVector

Dependencies:abind backports boot broom car carData cli colorspace combinat corrplot cowplot cpp11 curl Deriv doBy dplyr fansi farver Formula generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband jsonlite labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mc2d mgcv microbenchmark minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom purrr quantmod quantreg R6 RColorBrewer Rcpp RcppEigen rlang rstatix scales SparseM stringi stringr survival tibble tidyr tidyselect TTR utf8 vctrs viridisLite withr xts zoo

CloneSeeker

Rendered fromCloneSeeker.Rnwusingutils::Sweaveon Nov 19 2024.

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

Citation

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