pedtools - Creating and Working with Pedigrees and Marker Data
A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
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pedigreespedsuite
8.97 score 28 stars 18 dependents 103 scripts 631 downloads
forrel - Forensic Pedigree Analysis and Relatedness Inference
Forensic applications of pedigree analysis, including likelihood ratios for relationship testing, general relatedness inference, marker simulation, and power analysis. 'forrel' is part of the 'pedsuite', a collection of packages for pedigree analysis, further described in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302). Several functions deal specifically with power analysis in missing person cases, implementing methods described in Vigeland et al. (2020) <doi:10.1016/j.fsigen.2020.102376>. Data import from the 'Familias' software (Egeland et al. (2000) <doi:10.1016/S0379-0738(00)00147-X>) is supported through the 'pedFamilias' package.
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forensic-geneticskinship-testingpedigree-analysispedsuiterelatedness
6.95 score 12 stars 7 dependents 89 scripts 435 downloadspedsuite - Easy Installation of the 'pedsuite' Packages for Pedigree Analysis
The 'pedsuite' is a collection of packages for pedigree analysis, covering applications in forensic genetics, medical genetics and more. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN: 9780128244302).
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6.11 score 16 stars 40 scripts 260 downloads
pedprobr - Probability Computations on Pedigrees
An implementation of the Elston-Stewart algorithm for calculating pedigree likelihoods given genetic marker data (Elston and Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is extended to allow inbred founders. 'pedprobr' is part of the 'pedsuite', a collection of packages for pedigree analysis in R. In particular, 'pedprobr' depends on 'pedtools' for pedigree manipulations and 'pedmut' for mutation modelling. For more information, see 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
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5.60 score 4 stars 11 dependents 6 scripts 992 downloads
ibdsim2 - Simulation of Chromosomal Regions Shared by Family Members
Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Halldorsson et al. (2019) <doi:10.1126/science.aau1043>), phased chromosomes are simulated for all pedigree members. Applications include calculation of realised relatedness coefficients and IBD segment distributions. 'ibdsim2' is part of the 'pedsuite' collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite', including a separate chapter on 'ibdsim2', is available in the book 'Pedigree analysis in R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising and comparing IBD distributions is available at <https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
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identity-by-descentrelatednesssimulationcpp
5.55 score 6 stars 2 dependents 28 scripts 411 downloadspedmut - Mutation Models for Pedigree Likelihood Computations
A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include equal, proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
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mutation-modelingpedigree-analysispedsuite
5.26 score 3 stars 20 dependents 7 scripts 1.0k downloads
ribd - Pedigree-based Relatedness Coefficients
Recursive algorithms for computing various relatedness coefficients, including pairwise kinship, kappa and identity coefficients. Both autosomal and X-linked coefficients are computed. Founders are allowed to be inbred, which enables construction of any given kappa coefficients, as described in Vigeland (2020) <doi:10.1007/s00285-020-01505-x>. In addition to the standard coefficients, 'ribd' also computes a range of lesser-known coefficients, including generalised kinship coefficients, multi-person coefficients and two-locus coefficients (Vigeland, 2023, <doi:10.1093/g3journal/jkac326>). Many features of 'ribd' are available through the online app 'QuickPed' at <https://magnusdv.shinyapps.io/quickped>; see Vigeland (2022) <doi:10.1186/s12859-022-04759-y>.
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inbreeding-coefficientkinshippedigree-analysispedsuiterelatedness
5.10 score 7 stars 11 dependents 11 scripts 712 downloadsdvir - Disaster Victim Identification
Joint DNA-based disaster victim identification (DVI), as described in Vigeland and Egeland (2021) <doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by optimising the joint likelihood of all victim samples and reference individuals. Individual identification probabilities, conditional on all available information, are derived from the joint solution in the form of posterior pairing probabilities. 'dvir' is part of the 'pedsuite' collection of packages for pedigree analysis.
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dviforensic-geneticskinship-testingpedsuite
4.88 score 3 stars 1 dependents 21 scripts 768 downloadsibdfindr - 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.
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4.68 score 4 stars 1 dependents 4 scripts 498 downloadspedFamilias - Import and Export 'Familias' Files
Tools for exchanging pedigree data between the 'pedsuite' packages and the 'Familias' software for forensic kinship computations (Egeland et al. (2000) <doi:10.1016/s0379-0738(00)00147-x>). These functions were split out from the 'forrel' package to streamline maintenance and provide a lightweight alternative for packages otherwise independent of 'forrel'.
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familiaskinship-testingpedsuite
4.38 score 2 stars 4 dependents 5 scripts 334 downloadsverbalisr - Describe Pedigree Relationships in Words
Describe in words the genealogical relationship between two members of a given pedigree, using the algorithm in Vigeland (2022) <doi:10.1186/s12859-022-04759-y>. 'verbalisr' is part of the 'pedsuite' collection of packages for pedigree analysis. For a demonstration of 'verbalisr', see the online app 'QuickPed' at <https://magnusdv.shinyapps.io/quickped>.
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genealogypedigree-analysispedsuiterelatedness
4.08 score 1 stars 8 dependents 7 scripts 414 downloadsparamlink2 - Parametric Linkage Analysis
Parametric linkage analysis of monogenic traits in medical pedigrees. Features include singlepoint analysis, multipoint analysis via 'MERLIN' (Abecasis et al. (2002) <doi:10.1038/ng786>), visualisation of log of the odds (LOD) scores and summaries of linkage peaks. Disease models may be specified to accommodate phenocopies, reduced penetrance and liability classes. 'paramlink2' is part of the 'pedsuite' package ecosystem, presented in 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
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3.88 score 5 stars 1 dependents 5 scripts 185 downloadssegregatr - Segregation Analysis for Variant Interpretation
An implementation of the full-likelihood Bayes factor (FLB) for evaluating segregation evidence in clinical medical genetics. The method was introduced by Thompson et al. (2003) <doi:10.1086/378100>. This implementation supports custom penetrance values and liability classes, and allows visualisations and robustness analysis as presented in Ratajska et al. (2023) <doi:10.1002/mgg3.2107>. See also the online app 'shinyseg', <https://chrcarrizosa.shinyapps.io/shinyseg>, which offers interactive segregation analysis with many additional features (Carrizosa et al. (2024) <doi:10.1093/bioinformatics/btae201>).
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medical-geneticspedigree-analysispedsuitesegregation-analysisvariant-interpretation
3.73 score 3 stars 1 dependents 12 scripts 287 downloadspedbuildr - Pedigree Reconstruction
Reconstruct pedigrees from genotype data, by optimising the likelihood over all possible pedigrees subject to given restrictions. Tailor-made plots facilitate evaluation of the output. This package is part of the 'pedsuite' ecosystem for pedigree analysis. In particular, it imports 'pedprobr' for calculating pedigree likelihoods and 'forrel' for estimating pairwise relatedness.
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pedigree-reconstructionpedsuiterelatednessrelationship-prediction
3.65 score 3 stars 1 dependents 7 scripts 246 downloadsnorSTR - Allele Frequencies for 50 Forensic STR Markers
Allele frequency databases for 50 forensic short tandem repeat (STR) markers, covering Norway and several broader regional populations: Europe, Africa, South America, West Asia, Middle Asia, and East Asia. Developed and maintained for use at the Department of Forensic Sciences, Oslo, Norway.
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3.48 score 2 dependents 4 scripts 633 downloadsKLINK - Kinship Analysis with Linked Markers
A 'shiny' application for forensic kinship testing, based on the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R) software 'Familias' and 'FamLink', but offers several unique features, including visualisations and automated report generation. The calculation of likelihood ratios supports pairs of linked markers, and all common mutation models.
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forensic-geneticskinship-testingpedsuiteshiny
3.30 score 1 stars 5 scripts 471 downloads