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

1.0.2Package record

Adaptive Base Error Model in Ultra-Deep Sequencing Data

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Nicola CasiraghiCRAN 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.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 47 wordsVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

abemus 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

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Nicola Casiraghi

Author, Maintainer since 1.0.1 (2019)

Alessandro Romanel

Author

Francesco Orlando

Contributor

Francesca Demichelis

Contributor

Releases (2)

Pick two releases to compare their code metrics.

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

Package metadata

First published: 2019-12-02
Total releases: 2 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.3 MB / 5 files

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 October 27, 2026, from https://CRAN.R-project.org/package=abemus

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 abemus version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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