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pedsuite: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).
Maintained by Magnus Dehli Vigeland. Last updated 5 months ago.
57.1 match 12 stars 5.98 score 23 scriptsmagnusdv
pedFamilias: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'.
Maintained by Magnus Dehli Vigeland. Last updated 6 months ago.
familiaskinship-testingpedsuite
10.5 match 2 stars 4.56 score 5 scripts 6 dependentsmagnusdv
KLINK: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.
Maintained by Magnus Dehli Vigeland. Last updated 7 days ago.
forensic-geneticskinship-testingpedsuiteshiny
10.5 match 1 stars 3.88 score 5 scriptsmagnusdv
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).
Maintained by Magnus Dehli Vigeland. Last updated 2 months ago.
0.8 match 25 stars 8.83 score 60 scripts 18 dependentsmagnusdv
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/>.
Maintained by Magnus Dehli Vigeland. Last updated 15 days ago.
identity-by-descentrelatednesssimulationcpp
0.8 match 5 stars 5.00 score 19 scripts 1 dependentsmagnusdv
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.
Maintained by Magnus Dehli Vigeland. Last updated 6 days ago.
0.5 match 11 stars 6.98 score 63 scripts 7 dependentsmagnusdv
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).
Maintained by Magnus Dehli Vigeland. Last updated 4 days ago.
0.5 match 4 stars 5.77 score 6 scripts 11 dependentsmagnusdv
dvir: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.
Maintained by Magnus Dehli Vigeland. Last updated 3 months ago.
0.5 match 3 stars 5.05 score 21 scripts 1 dependentsmagnusdv
verbalisr: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>.
Maintained by Magnus Dehli Vigeland. Last updated 3 days ago.
pedigree-analysisrelatednessrelationship-detection
0.5 match 1 stars 4.92 score 7 scripts 8 dependentsmagnusdv
pedbuildr: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.
Maintained by Magnus Dehli Vigeland. Last updated 2 months ago.
0.5 match 2 stars 3.78 score 7 scripts 1 dependentsmagnusdv
paramlink2: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).
Maintained by Magnus Dehli Vigeland. Last updated 6 months ago.
0.5 match 3 stars 3.65 score 5 scripts 1 dependents