R Observatory: Metrics for CHAT version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2018-05-03. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.1, its last release before removal.

CHAT

1.1Package record

Clonal Heterogeneity Analysis Tool

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Bo LiCRAN page ↗Website ↗

CHAT is a collection of tools developed for tumor subclonality analysis using high density DNA SNP array data and sequencing data. The pipeline consists of four major compartments: 1) tumor aneuploid genome proportion (AGP) calculation and ploidy estimation. 2) segment-specific AGP calculation and absolute copy number estimation for somatic CNAs. 3) cancer cell fraction correction for somatic SNVs in clonal or subclonal sCNA regions. 4) number of subclones estimation using Dirichlet process prior followed by MCMC approach.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/CHAT/CHAT_1.1.tar.gz"
pkgFile <- "CHAT_1.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 44includes a package overview page
Examples that run: 53%20 run in a plain check · 15 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 97%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 7%

How these are measured

Downloads

CHAT Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (4)

R >= 2.10parallelDNAcopy DPpackage

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Bo Li

Contributor

Maintainer since 1.0 (2014)

Releases (2)

Pick two releases to compare their code metrics.

R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2018-05-03
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
1.1
record
2014-02-10 · diff ↗
1.0
record
2014-02-10
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-02-10
Total releases: 2 / 12 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 3.6 MB / 5 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CHAT")

Format

Li, B. (n.d.). CHAT: Clonal Heterogeneity Analysis Tool (Version 1.1) [Computer software]. Retrieved October 23, 2026, from https://CRAN.R-project.org/package=CHAT

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for CHAT version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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