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Canopy
View on CRAN: Click
here
Download and install Canopy package within the R console
Install from CRAN:
install.packages("Canopy")
Install from Github:
library("remotes")
install_github("cran/Canopy")
Install by package version:
library("remotes")
install_version("Canopy", "1.3.0")
Attach the package and use:
library("Canopy")
Maintained by
Yuchao Jiang
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-10-29
Latest Update: 2017-12-18
Description:
A statistical framework and computational procedure for identifying
the sub-populations within a tumor, determining the mutation profiles of each
subpopulation, and inferring the tumor's phylogenetic history. The input are
variant allele frequencies (VAFs) of somatic single nucleotide alterations
(SNAs) along with allele-specific coverage ratios between the tumor and matched
normal sample for somatic copy number alterations (CNAs). These quantities can
be directly taken from the output of existing software. Canopy provides a
general mathematical framework for pooling data across samples and sites to
infer the underlying parameters. For SNAs that fall within CNA regions, Canopy
infers their temporal ordering and resolves their phase. When there are
multiple evolutionary configurations consistent with the data, Canopy outputs
all configurations along with their confidence assessment.
How to cite:
Yuchao Jiang (2015). Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing. R package version 1.3.0, https://cran.r-project.org/web/packages/Canopy
Previous versions and publish date:
Other packages that cited Canopy R package
View Canopy citation profile
Other R packages that Canopy depends,
imports, suggests or enhances
Functions, R codes and Examples using
the Canopy R package
Some associated functions: AML43 . MDA231 . MDA231_sampchain . MDA231_tree . addsamptree . canopy.BIC . canopy.cluster.Estep . canopy.cluster.Mstep . canopy.cluster . canopy.output . canopy.plottree . canopy.post . canopy.sample.cluster.nocna . canopy.sample.cluster . canopy.sample.nocna . canopy.sample . getCMCm . getCZ . getQ . getVAF . getZ . getclonalcomposition . getlikelihood . getlikelihood.sna . initialP . initialcna . initialcnacopy . initialsna . sampP . sampcna . sampcnacopy . sampsna.cluster . sampsna . sortcna . toy . toy2 . toy3 .
Some associated R codes: addsamptree.R . canopy.BIC.R . canopy.cluster.Estep.R . canopy.cluster.Mstep.R . canopy.cluster.R . canopy.output.R . canopy.plottree.R . canopy.post.R . canopy.sample.R . canopy.sample.cluster.R . canopy.sample.cluster.nocna.R . canopy.sample.nocna.R . getCMCm.R . getCZ.R . getQ.R . getVAF.R . getZ.R . getclonalcomposition.R . getlikelihood.R . getlikelihood.sna.R . initialP.R . initialcna.R . initialcnacopy.R . initialsna.R . sampP.R . sampcna.R . sampcnacopy.R . sampsna.R . sampsna.cluster.R . sortcna.R . Full Canopy package functions and examples
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