Package: CloneSeeker 1.0.16

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:Mark Zucker [aut], Kevin R. Coombes [aut, cre]

CloneSeeker_1.0.16.tar.gz
CloneSeeker_1.0.16.tar.gz(r-4.7-any)CloneSeeker_1.0.16.tar.gz(r-4.6-any)
CloneSeeker_1.0.16.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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

On CRAN:

2.00 score 8 scripts 194 downloads 11 exports 85 dependencies

Last updated from:6351cc6cce. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	207
source / vignettes	OK	200
linux-release-x86_64	OK	215
wasm-release	OK	119

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 farver forecast Formula fracdiff generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband jsonlite labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mc2d mgcv microbenchmark minqa modelr mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom purrr quantmod quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rstatix S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate TTR urca utf8 vctrs viridisLite withr xts zoo

CloneSeeker

Rendered fromCloneSeeker.Rnwusingutils::Sweave

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

Package: CloneSeeker 1.0.16

CloneSeeker: Seeking and Finding Clones in Copy Number and Sequencing Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)