Showing 100 of total 100 results (show query)
jiscah
sequoia:Pedigree Inference from SNPs
Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Maintained by Jisca Huisman. Last updated 9 months ago.
pedigreepedigree-reconstructionpedigreessequoiasnpsnp-datafortran
81.2 match 26 stars 7.40 score 79 scripts
magnusdv
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.
65.3 match 25 stars 8.83 score 60 scripts 18 dependents
bioc
Pedixplorer:Pedigree Functions
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Maintained by Louis Le Nezet. Last updated 1 days ago.
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
82.3 match 2 stars 6.08 score 10 scripts
r-computing-lab
BGmisc:An R Package for Extended Behavior Genetics Analysis
Provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>], calculation of relatedness coefficients using path-tracing methods [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview, see Garrison et al. (2024) <doi:10.21105/joss.06203>.
Maintained by S. Mason Garrison. Last updated 24 days ago.
72.6 match 1 stars 6.83 score 35 scripts
matthewwolak
nadiv:(Non)Additive Genetic Relatedness Matrices
Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml>).
Maintained by Matthew Wolak. Last updated 10 months ago.
46.4 match 20 stars 7.13 score 151 scripts 3 dependents
albartcoster
pedigree:Pedigree Functions
Pedigree related functions.
Maintained by Albart Coster. Last updated 3 years ago.
71.1 match 3.88 score 85 scripts 3 dependents
mikldk
malan:MAle Lineage ANalysis
MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches. Refer to papers mentioned in citation("malan") (DOI's: <doi:10.1371/journal.pgen.1007028>, <doi:10.21105/joss.00684> and <doi:10.1016/j.fsigen.2018.10.004>).
Maintained by Mikkel Meyer Andersen. Last updated 1 years ago.
55.9 match 4.48 score 6 scriptsbioc
GeneticsPed:Pedigree and genetic relationship functions
Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!
Maintained by David Henderson. Last updated 5 months ago.
54.9 match 3.86 score 12 scriptsbioc
FamAgg:Pedigree Analysis and Familial Aggregation
Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.
Maintained by Johannes Rainer. Last updated 5 months ago.
34.7 match 1 stars 5.26 score 5 scripts
anainesvs
pedigreemm:Pedigree-Based Mixed-Effects Models
Fit pedigree-based mixed-effects models.
Maintained by Ana Ines Vazquez. Last updated 1 years ago.
32.0 match 1 stars 5.42 score 87 scripts 2 dependents
kbroman
simcross:Simulate Experimental Crosses
Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Maintained by Karl W Broman. Last updated 9 days ago.
33.8 match 6 stars 5.06 score 19 scripts
rramadeu
AGHmatrix:Relationship Matrices for Diploid and Autopolyploid Species
Computation of A (pedigree), G (genomic-base), and H (A corrected by G) relationship matrices for diploid and autopolyploid species. Several methods are implemented considering additive and non-additive models.
Maintained by Rodrigo Amadeu. Last updated 4 months ago.
18.6 match 11 stars 7.80 score 102 scripts 2 dependents
rpedigree
pedigreeTools:Versatile Functions for Working with Pedigrees
Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients and the relationship matrix (includes code for pedigrees from self-pollinated species). The use of pedigree data is central to genetics research within the animal and plant breeding communities to predict breeding values. The relationship matrix between the individuals can be derived from pedigree structure ('Vazquez et al., 2010') <doi:10.2527/jas.2009-1952>.
Maintained by Paulino Perez Rodriguez. Last updated 1 years ago.
29.1 match 11 stars 4.69 score 15 scripts
jinghuazhao
gap:Genetic Analysis Package
As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).
Maintained by Jing Hua Zhao. Last updated 16 days ago.
10.4 match 12 stars 11.88 score 448 scripts 16 dependents
famuvie
breedR:Statistical Methods for Forest Genetic Resources Analysts
Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.
Maintained by Facundo Muñoz. Last updated 8 months ago.
20.2 match 33 stars 5.44 score 24 scripts
eriqande
gscramble:Simulating Admixed Genotypes Without Replacement
A genomic simulation approach for creating biologically informed individual genotypes from empirical data that 1) samples alleles from populations without replacement, 2) segregates alleles based on species-specific recombination rates. 'gscramble' is a flexible simulation approach that allows users to create pedigrees of varying complexity in order to simulate admixed genotypes. Furthermore, it allows users to track haplotype blocks from the source populations through the pedigrees.
Maintained by Eric C. Anderson. Last updated 1 years ago.
22.5 match 4.83 score 15 scriptsmagnusdv
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>.
Maintained by Magnus Dehli Vigeland. Last updated 1 months ago.
inbreeding-coefficientkinshippedigree-analysisrelatedness
17.4 match 6 stars 5.95 score 10 scripts 11 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 2 days ago.
pedigree-analysisrelatednessrelationship-detection
15.9 match 1 stars 4.92 score 7 scripts 8 dependentsbioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilityqualitycontrolmicroarray
7.5 match 17 stars 10.50 score 396 scripts 5 dependents
cran
purgeR:Inbreeding-Purging Estimation in Pedigreed Populations
Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.
Maintained by Eugenio López-Cortegano. Last updated 1 years ago.
30.8 match 2.41 score 13 scripts
juliengamartin
pedtricks:Visualize, Summarize and Simulate Data from Pedigrees
Sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for visualizing pedigrees. This is a reboot of the methods developped by Morrissey and Wilson (2010) <doi: 10.1111/j.1755-0998.2009.02817.x>
Maintained by Julien Martin. Last updated 6 months ago.
18.2 match 2 stars 4.08 score 1 scriptsbioc
RVS:Computes estimates of the probability of related individuals sharing a rare variant
Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).
Maintained by Alexandre Bureau. Last updated 5 months ago.
immunooncologygeneticsgenomewideassociationvariantdetectionexomeseqwholegenome
14.3 match 4.78 score 9 scriptsbioc
AlphaBeta:Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging.
Maintained by Yadollah Shahryary Dizaji. Last updated 5 months ago.
epigeneticsfunctionalgenomicsgeneticsmathematicalbiology
14.0 match 4.85 score 8 scripts
nilforooshan
ggroups:Pedigree and Genetic Groups
Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, calculating inbreeding coefficients (Meuwissen & Luo, 1992 <doi:10.1186/1297-9686-24-4-305>), as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Maintained by Mohammad Ali Nilforooshan. Last updated 6 months ago.
23.6 match 1 stars 2.70 score 2 scriptsbioc
MinimumDistance:A Package for De Novo CNV Detection in Case-Parent Trios
Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
Maintained by Robert Scharpf. Last updated 5 months ago.
microarraysnpcopynumbervariation
16.3 match 3.60 score 10 scripts
jarrodhadfield
MCMCglmm:MCMC Generalised Linear Mixed Models
Fits Multivariate Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. Soft.).
Maintained by Jarrod Hadfield. Last updated 3 months ago.
6.3 match 2 stars 8.83 score 1.2k scripts 13 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 5 days ago.
7.5 match 11 stars 6.98 score 63 scripts 7 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.
13.6 match 2 stars 3.78 score 7 scripts 1 dependents
thoree
Familias:Probabilities for Pedigrees Given DNA Data
An interface to the core 'Familias' functions which are programmed in C++. The implementation is described in Egeland, Mostad and Olaisen (1997) <doi:10.1016/S1355-0306(97)72202-0> and Simonsson and Mostad (2016) <doi:10.1016/j.fsigen.2016.04.005>.
Maintained by Thore Egeland. Last updated 2 months ago.
8.5 match 8 stars 6.00 score 14 scripts 1 dependents
ekstroem
MESS:Miscellaneous Esoteric Statistical Scripts
A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book. See Ekstrøm, C. T. (2016). The R Primer. 2nd edition. Chapman & Hall.
Maintained by Claus Thorn Ekstrøm. Last updated 29 days ago.
biostatisticspower-analysisstatistical-analysisstatistical-methodsstatistical-modelsopenblascpp
6.5 match 4 stars 7.76 score 328 scripts 13 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 3 days ago.
8.5 match 4 stars 5.77 score 6 scripts 11 dependents
gaynorr
AlphaSimR:Breeding Program Simulations
The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Maintained by Chris Gaynor. Last updated 5 months ago.
breedinggenomicssimulationopenblascppopenmp
4.5 match 47 stars 10.22 score 534 scripts 2 dependents
signaturescience
skater:Utilities for SNP-Based Kinship Analysis
Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.
Maintained by Stephen Turner. Last updated 2 years ago.
8.3 match 9 stars 5.26 score 7 scriptscran
hsphase:Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Maintained by Mohammad Ferdosi. Last updated 1 years ago.
12.3 match 1 stars 3.32 score 1 dependentsbioc
RAIDS:Accurate Inference of Genetic Ancestry from Cancer Sequences
This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
Maintained by Pascal Belleau. Last updated 5 months ago.
geneticssoftwaresequencingwholegenomeprincipalcomponentgeneticvariabilitydimensionreductionbiocviewsancestrycancer-genomicsexome-sequencinggenomicsinferencer-languagerna-seqrna-sequencingwhole-genome-sequencing
6.4 match 5 stars 6.23 score 19 scripts
kwstat
agridat:Agricultural Datasets
Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
Maintained by Kevin Wright. Last updated 28 days ago.
3.6 match 125 stars 11.02 score 1.7k scripts 2 dependentscran
BGLR:Bayesian Generalized Linear Regression
Bayesian Generalized Linear Regression.
Maintained by Paulino Perez Rodriguez. Last updated 5 months ago.
7.5 match 2 stars 5.18 score 5 dependentsnilforooshan
pedMermaid:Pedigree Mermaid Syntax
Generate Mermaid syntax for a pedigree flowchart from a pedigree data frame. Mermaid syntax is commonly used to generate plots, charts, diagrams, and flowcharts. It is a textual syntax for creating reproducible illustrations. This package generates Mermaid syntax from a pedigree data frame to visualize a pedigree flowchart. The Mermaid syntax can be embedded in a Markdown or R Markdown file, or viewed on Mermaid editors and renderers. Links' shape, style, and orientation can be customized via function arguments, and nodes' shapes and styles can be customized via optional columns in the pedigree data frame.
Maintained by Mohammad Ali Nilforooshan. Last updated 6 months ago.
7.8 match 2 stars 4.60 scorebioc
SeqVarTools:Tools for variant data
An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilitysequencinggenetics
4.0 match 3 stars 8.76 score 384 scripts 2 dependents
roelandv
PolyHaplotyper:Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids
Infer the genetic composition of individuals in terms of haplotype dosages for a haploblock, based on bi-allelic marker dosages, for any ploidy level. Reference: Voorrips and Tumino: PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. Submitted to BMC Bioinformatics (2021).
Maintained by Roeland E. Voorrips. Last updated 4 years ago.
17.3 match 2.00 score 3 scriptsnilforooshan
pedSimulate:Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes. Mrode, R. A. (2005) <ISBN:9780851989969, 0851989969>; Nilforooshan, M.A. (2022) <doi:10.37496/rbz5120210131>.
Maintained by Mohammad Ali Nilforooshan. Last updated 6 months ago.
11.2 match 2 stars 3.00 score
marsicofl
fbnet:Forensic Bayesian Networks
Open-source package for computing likelihood ratios in kinship testing and human identification cases (Chernomoretz et al. (2021) <doi:10.1016/j.fsir.2020.100132>). It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals (Darwiche (2009) <doi:10.1017/CBO9780511811357>).
Maintained by Franco Marsico. Last updated 1 years ago.
10.4 match 1 stars 3.18 score 4 scripts 1 dependents
sinnweja
pedgene:Gene-Level Variant Association Tests for Pedigree Data
Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.
Maintained by Jason Sinnwell. Last updated 11 months ago.
8.6 match 3.78 score 6 scripts 1 dependents
weiguonimh
rvHPDT:Calling Haplotype-Based and Variant-Based Pedigree Disequilibrium Test for Rare Variants in Pedigrees
To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.
Maintained by Wei Guo. Last updated 3 years ago.
15.2 match 2.00 score 2 scripts
icarda-git
QBMS:Query the Breeding Management System(s)
This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Maintained by Khaled Al-Shamaa. Last updated 6 months ago.
3.9 match 8 stars 7.85 score 33 scripts 1 dependentsmagnusdv
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.
5.0 match 12 stars 5.98 score 23 scripts
tpook92
MoBPS:Modular Breeding Program Simulator
Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. The package is also used as the background simulator for our a web-based interface <http:www.mobps.de>. Associated publication: Pook et al. (2020) <doi:10.1534/g3.120.401193>.
Maintained by Torsten Pook. Last updated 3 years ago.
12.5 match 2.35 score 45 scripts
jgdowty
clipp:Calculating Likelihoods by Pedigree Paring
A fast and general implementation of the Elston-Stewart algorithm that can calculate the likelihoods of large and complex pedigrees. References for the Elston-Stewart algorithm are Elston & Stewart (1971) <doi:10.1159/000152448>, Lange & Elston (1975) <doi:10.1159/000152714> and Cannings et al. (1978) <doi:10.2307/1426718>.
Maintained by James Dowty. Last updated 3 years ago.
10.1 match 2.48 score 3 scripts 1 dependents
xiaolei-lab
simer:Data Simulation for Life Science and Breeding
Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.
Maintained by Xiaolei Liu. Last updated 18 days ago.
4.3 match 28 stars 5.80 score 2 scriptscran
GESE:Gene-Based Segregation Test
Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). <DOI:10.1002/gepi.22037>. Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Maintained by Dandi Qiao. Last updated 8 years ago.
11.8 match 2.08 score 12 scriptsekstroem
networkR:Network Analysis and Visualization
Collection of functions for fast manipulation, handling, and analysis of large-scale networks based on family and social data. Functions are utility functions used to manipulate data in three "formats": sparse adjacency matrices, pedigree trio family data, and pedigree family data. When possible, the functions should be able to handle millions of data points quickly for use in combination with data from large public national registers and databases. Kenneth Lange (2003, ISBN:978-8181281135).
Maintained by Claus Thorn Ekstrøm. Last updated 5 years ago.
network-analysisnetwork-visualizationcpp
6.0 match 7 stars 3.62 score 12 scripts
jangraffelman
Jacquard:Estimation of Jacquard's Genetic Identity Coefficients
Contains procedures to estimate the nine condensed Jacquard genetic identity coefficients (Jacquard, 1974) <doi:10.1007/978-3-642-88415-3> by constrained least squares (Graffelman et al., 2024) <doi:10.1101/2024.03.25.586682> and by the method of moments (Csuros, 2014) <doi:10.1016/j.tpb.2013.11.001>. These procedures require previous estimation of the allele frequencies. Functions are supplied that estimate relationship parameters that derive from the Jacquard coefficients, such as individual inbreeding coefficients and kinship coefficients.
Maintained by Jan Graffelman. Last updated 6 months ago.
10.6 match 2.00 scoremagnusdv
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.
4.1 match 3 stars 5.05 score 21 scripts 1 dependents
sgezan
ASRgenomics:Complementary Genomic Functions
Presents a series of molecular and genetic routines in the R environment with the aim of assisting in analytical pipelines before and after the use of 'asreml' or another library to perform analyses such as Genomic Selection or Genome-Wide Association Analyses. Methods and examples are described in Gezan, Oliveira, Galli, and Murray (2022) <https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASRgenomics_Manual.pdf>.
Maintained by Salvador Gezan. Last updated 1 years ago.
8.8 match 1 stars 2.28 score 38 scripts
nevillejackson
dmm:Dyadic Mixed Model for Pedigree Data
Mixed model analysis for quantitative genetics with multi-trait responses and pedigree-based partitioning of individual variation into a range of environmental and genetic variance components for individual and maternal effects. Method documented in dmmOverview.pdf; dmm is an implementation of dispersion mean model described by Searle et al. (1992) "Variance Components", Wiley, NY. 'DMM' can do 'MINQUE', 'bias-corrected-ML', and 'REML' variance component estimates.
Maintained by Neville Jackson. Last updated 19 days ago.
7.0 match 2 stars 2.74 score 71 scripts
mkruijver
simDNAmixtures:Simulate Forensic DNA Mixtures
Mixed DNA profiles can be sampled according to models for probabilistic genotyping. Peak height variability is modelled using a log normal distribution or a gamma distribution. Sample contributors may be related according to a pedigree.
Maintained by Maarten Kruijver. Last updated 3 months ago.
3.8 match 5.04 score 9 scripts
bowenwang7
rres:Realized Relatedness Estimation and Simulation
Functions for studying realized genetic relatedness between people. Users will be able to simulate inheritance patterns given pedigree structures, generate SNP marker data given inheritance patterns, and estimate realized relatedness between pairs of individuals using SNP marker data. See Wang (2017) <doi:10.1534/genetics.116.197004>. This work was supported by National Institutes of Health grants R37 GM-046255.
Maintained by Bowen Wang. Last updated 7 years ago.
6.4 match 2.95 score 18 scriptseriqande
CKMRpop:Forward-in-Time Simulation and Tallying of Pairwise Relationships
Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.
Maintained by Eric C. Anderson. Last updated 1 years ago.
3.4 match 4 stars 5.38 score 24 scripts
cjgeyer
sped:Multi-Gene Descent Probabilities
Do multi-gene descent probabilities (Thompson, 1983, <doi:10.1098/rspb.1983.0072>) and special cases thereof (Thompson, 1986, <doi:10.1002/zoo.1430050210>) including inbreeding and kinship coefficients. But does much more: probabilities of any set of genes descending from any other set of genes.
Maintained by Charles J. Geyer. Last updated 2 years ago.
7.6 match 2.28 score 19 scriptsalbartcoster
HaploSim:Functions to Simulate Haplotypes
Simulate haplotypes through meioses. Allows specification of population parameters.
Maintained by Albart Coster. Last updated 3 years ago.
5.4 match 3.20 score 12 scripts 4 dependentsmagnusdv
pedmut: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.
Maintained by Magnus Dehli Vigeland. Last updated 1 years ago.
3.5 match 2 stars 4.76 score 5 scripts 19 dependents
vincentgarin
mppR:Multi-Parent Population QTL Analysis
Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits measured in unique and multiple environments. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) <doi:10.1007/s00122-017-2923-3>, in Garin, Malosetti and van Eeuwijk (2020) <doi: 10.1007/s00122-020-03621-0>, and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) <doi: 10.1093/genetics/iyae003>.
Maintained by Vincent Garin. Last updated 1 years ago.
3.0 match 2 stars 5.35 score 28 scriptscran
GENLIB:Genealogical Data Analysis
Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) <doi:10.1186/s12859-015-0581-5>.
Maintained by Marie-Helene Roy-Gagnon. Last updated 1 years ago.
8.0 match 1.78 score 1 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 13 days ago.
identity-by-descentrelatednesssimulationcpp
2.8 match 5 stars 5.00 score 19 scripts 1 dependents
cran
pbatR:Pedigree/Family-Based Genetic Association Tests Analysis and Power
This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Maintained by Thomas Hoffmann. Last updated 1 years ago.
6.9 match 2 stars 1.78 score 7 scripts 1 dependents
diondetterer
epinetr:Epistatic Network Modelling with Forward-Time Simulation
Allows for forward-in-time simulation of epistatic networks with associated phenotypic output.
Maintained by Dion Detterer. Last updated 3 years ago.
3.3 match 3.70 score 9 scripts
warnes
genetics:Population Genetics
Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...
Maintained by Gregory Warnes. Last updated 4 years ago.
2.0 match 2 stars 5.55 score 374 scripts 5 dependentscran
AlphaPart:Partition/Decomposition of Breeding Values by Paths of Information
A software that implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes. The partitioning method is described in Garcia-Cortes et al. (2008) <doi:10.1017/S175173110800205X>. The package includes the main function AlphaPart for partitioning breeding values and auxiliary functions for manipulating data and summarizing, visualizing, and saving results.
Maintained by Gregor Gorjanc. Last updated 2 years ago.
4.0 match 2.72 score 26 scripts
pbiecek
archivist:Tools for Storing, Restoring and Searching for R Objects
Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Maintained by Przemyslaw Biecek. Last updated 7 months ago.
1.2 match 74 stars 8.81 score 105 scripts 2 dependents
f-rousset
spaMM:Mixed-Effect Models, with or without Spatial Random Effects
Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Maintained by François Rousset. Last updated 9 months ago.
1.8 match 4.94 score 208 scripts 5 dependentscran
IBDsim: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 (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.
Maintained by Magnus Dehli Vigeland. Last updated 6 years ago.
4.8 match 1.78 score
biometris
statgenIBD:Calculation of IBD Probabilities
For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (<https://www.jstor.org/stable/29713>) and Huang (<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Maintained by Bart-Jan van Rossum. Last updated 1 months ago.
1.5 match 5.26 score 8 scripts 1 dependents
jl5000
visged:Visualise GEDCOM Files
Produce a variety of visualisations for family tree GEDCOM files.
Maintained by Jamie Lendrum. Last updated 3 years ago.
3.5 match 2.18 score 3 scripts 1 dependentsmagnusdv
segregatr: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>).
Maintained by Magnus Dehli Vigeland. Last updated 9 months ago.
1.9 match 3 stars 4.03 score 12 scripts 1 dependentscran
BLR:Bayesian Linear Regression
Bayesian Linear Regression.
Maintained by Paulino Perez Rodriguez. Last updated 5 years ago.
3.8 match 2.00 score
guanju-ma
KINSIMU:Panel Evaluation in Forensic Kinship Analysis
Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
Maintained by Guanju Ma. Last updated 9 months ago.
2.8 match 2.70 score
nilforooshan
FnR:Inbreeding and Numerator Relationship Coefficients
Compute inbreeding coefficients using the method of Meuwissen and Luo (1992) <doi:10.1186/1297-9686-24-4-305>, and numerator relationship coefficients between individuals using the method of Van Vleck (2007) <https://pubmed.ncbi.nlm.nih.gov/18050089/>.
Maintained by Mohammad Ali Nilforooshan. Last updated 6 months ago.
1.7 match 1 stars 4.30 scorecran
sim1000G:Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Generates realistic simulated genetic data in families or unrelated individuals.
Maintained by Apostolos Dimitromanolakis. Last updated 6 years ago.
2.3 match 1 stars 2.78 score
covaruber
sommer:Solving Mixed Model Equations in R
Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 22 days ago.
average-informationmixed-modelsrcpparmadilloopenblascppopenmp
0.5 match 43 stars 12.70 score 300 scripts 9 dependents
elweiser
AlleleRetain:Allele Retention, Inbreeding, and Demography
Simulate the effect of management or demography on allele retention and inbreeding accumulation in bottlenecked populations of animals with overlapping generations.
Maintained by Emily Weiser. Last updated 7 years ago.
4.3 match 1.48 score 1 scripts
petergreen5678
KinMixLite:Inference About Relationships from DNA Mixtures
Methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. This provides most of the functionality of the 'KinMix' package, but with some loss of efficiency and restriction on problem size, as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'. The package implements the methods introduced in Green, P. J. and Mortera, J. (2017) <doi:10.1016/j.fsigen.2017.02.001> and Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.
Maintained by Peter Green. Last updated 5 months ago.
5.3 match 1.00 scorebioc
GENESIS:GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.
Maintained by Stephanie M. Gogarten. Last updated 1 months ago.
snpgeneticvariabilitygeneticsstatisticalmethoddimensionreductionprincipalcomponentgenomewideassociationqualitycontrolbiocviews
0.5 match 36 stars 10.44 score 342 scripts 1 dependentsmarsicofl
forensIT:Information Theory Tools for Forensic Analysis
The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Maintained by Franco Marsico. Last updated 1 months ago.
2.0 match 1.70 score 1 scriptsmagnusdv
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.
0.8 match 3 stars 3.65 score 5 scripts 1 dependentsmagnusdv
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
0.5 match 2 stars 4.56 score 5 scripts 6 dependents
kdpeterson51
mlf:Machine Learning Foundations
Offers a gentle introduction to machine learning concepts for practitioners with a statistical pedigree: decomposition of model error (bias-variance trade-off), nonlinear correlations, information theory and functional permutation/bootstrap simulations. Székely GJ, Rizzo ML, Bakirov NK. (2007). <doi:10.1214/009053607000000505>. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC. (2011). <doi:10.1126/science.1205438>.
Maintained by Kyle Peterson. Last updated 7 years ago.
0.5 match 1.08 score 12 scriptscran
GSSE:Genotype-Specific Survival Estimation
We propose a fully efficient sieve maximum likelihood method to estimate genotype-specific distribution of time-to-event outcomes under a nonparametric model. We can handle missing genotypes in pedigrees. We estimate the time-dependent hazard ratio between two genetic mutation groups using B-splines, while applying nonparametric maximum likelihood estimation to the reference baseline hazard function. The estimators are calculated via an expectation-maximization algorithm.
Maintained by Baosheng Liang. Last updated 9 years ago.
0.5 match 1.00 score