R Observatory: Metrics for abemus version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2019-12-20. Its history is shown below.

Reason: update had the same check problems as before

Details below reflect version 1.0.2, its last release before removal.

abemus

1.0.2

Adaptive Base Error Model in Ultra-Deep Sequencing Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Nicola Casiraghi2 releasesCRAN page ↗

The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/abemus/abemus_1.0.2.tar.gz"
pkgFile <- "abemus_1.0.2.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 (1.0.2) 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.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Documentation

READMEYes · 47 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

abemus Releases R versions

Daily download trend is not available in this view yet.

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Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (1)

data.table

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Nicola Casiraghi

Author, Maintainer

Authors (2)

Nicola Casiraghi

Author, Maintainer

Alessandro Romanel

Author

Contributors (2)

Francesco Orlando

Contributor

Francesca Demichelis

Contributor

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2019-12-20
update had the same check problems as before
1.0.2
2019-12-18 · diff ↗
unarchivedReturned to CRAN
2019-12-18
archivedRemoved from CRAN
2019-12-18
check problems were not corrected in time
1.0.1
2019-12-02
R
R 3.6.0 released · 2019-04-26

Package metadata

Total releases: 2
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.3 MB / 5 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("abemus")

Format

Casiraghi, N., Romanel, A., Orlando, F., & Demichelis, F. (n.d.). abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data (Version 1.0.2) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=abemus

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 abemus version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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