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ibdfindr: HMM Toolkit for Inferring IBD Segments from SNP Genotypes

Implements continuous-time hidden Markov models (HMMs) to infer identity-by-descent (IBD) segments shared by two individuals from their single-nucleotide polymorphism (SNP) genotypes. Provides posterior probabilities at each marker (forward-backward algorithm), prediction of IBD segments (Viterbi algorithm), and functions for visualising results. Supports both autosomal data and X-chromosomal data.

Version: 0.3.1
Depends: R (≥ 4.2)
Imports: forrel, ggplot2, ibdsim2, pedtools, ribd
Suggests: testthat (≥ 3.0.0)
Published: 2025-08-18
DOI: 10.32614/CRAN.package.ibdfindr
Author: Magnus Dehli Vigeland ORCID iD [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland at medisin.uio.no>
BugReports: https://github.com/magnusdv/ibdfindr/issues
License: GPL (≥ 3)
URL: https://github.com/magnusdv/ibdfindr
NeedsCompilation: no
Language: en-GB
Materials: README, NEWS
CRAN checks: ibdfindr results

Documentation:

Reference manual: ibdfindr.html , ibdfindr.pdf

Downloads:

Package source: ibdfindr_0.3.1.tar.gz
Windows binaries: r-devel: ibdfindr_0.3.1.zip, r-release: ibdfindr_0.3.1.zip, r-oldrel: ibdfindr_0.3.1.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): ibdfindr_0.3.1.tgz, r-oldrel (x86_64): ibdfindr_0.3.1.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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