Other packages > Find by keyword >

Canopy  

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing
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]
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. Accessed 17 Jul. 2026.
Previous versions and publish date:
1.0.0 (2015-10-29 18:50), 1.1.1 (2016-09-02 22:26), 1.2.0 (2017-04-08 22:30), 1.3.0 (2017-12-18 20:12), (2026-07-09 08:00)
Other packages that cited Canopy R package
View Canopy citation profile
Other R packages that Canopy depends, imports, suggests or enhances
Complete documentation for Canopy
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

VEwaningVariant  
Vaccine Efficacy Over Time - Variant Aware
Implements methods for inference on potential waning of vaccine efficacy and for estimation of vacci ...
Download / Learn more Package Citations See dependency  
FastKNN  
Fast k-Nearest Neighbors
Compute labels for a test set according to the k-Nearest Neighbors classification. This is a fast wa ...
Download / Learn more Package Citations See dependency  
rt.test  
Robustified t-Test
Performs one-sample t-test based on robustified statistics using median/MAD (TA) and Hodges-Lehmann/ ...
Download / Learn more Package Citations See dependency  
alabama  
Constrained Nonlinear Optimization
Augmented Lagrangian Adaptive Barrier Minimization Algorithm for optimizing smooth nonlinear object ...
Download / Learn more Package Citations See dependency  
VFS  
Vegetated Filter Strip and Erosion Model
Empirical models for runoff, erosion, and phosphorus loss across a vegetated filter strip, given sl ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA