CRAN/E | Canopy

Canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

Installation

About

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.

github.com/yuchaojiang/Canopy

Key Metrics

Version 1.3.0
R ≥ 3.4
Published 2017-12-18 2314 days ago
Needs compilation? no
License GPL-2
CRAN checks Canopy results

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Maintainer

Maintainer

Yuchao Jiang

yuchaoj@email.unc.edu

Authors

Yuchao Jiang
Nancy R. Zhang

Material

NEWS
Reference manual
Package source

Vignettes

Using Canopy

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

Canopy archive

Depends

R ≥ 3.4
ape
fields
pheatmap
scatterplot3d

Imports

grDevices
graphics
stats
utils