R-universe search: heterozygosity

kfarleigh

PopGenHelpR:Streamline Population Genomic and Genetic Analyses

Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.

Maintained by Keaka Farleigh. Last updated 8 months ago.

diversity fst heterozygosity interpolation neis population-genetics population-genomics private-alleles snmf structure vcf

30.9 match 3 stars 5.17 score 14 scripts

green-striped-gecko

dartR.base:Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism') and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility', maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.

Maintained by Bernd Gruber. Last updated 12 days ago.

23.2 match 3.84 score 17 scripts 5 dependents

mastoffel

inbreedR:Analysing Inbreeding Based on Genetic Markers

A framework for analysing inbreeding and heterozygosity-fitness correlations (HFCs) based on microsatellite and SNP markers.

Maintained by Martin A. Stoffel. Last updated 5 months ago.

9.9 match 3 stars 5.88 score 51 scripts

bioinformatics-ptp

detectRUNS:Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) <doi:10.1086/519795>) and consecutive runs (Marras et al (2015) <doi:10.1111/age.12259>).

Maintained by Filippo Biscarini. Last updated 3 years ago.

cpp

8.2 match 9 stars 6.50 score 35 scripts

thibautjombart

adegenet:Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Maintained by Zhian N. Kamvar. Last updated 1 months ago.

3.8 match 182 stars 12.60 score 1.9k scripts 29 dependents

bioc

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.

snp geneticvariability sequencing genetics

5.3 match 3 stars 8.76 score 384 scripts 2 dependents

meyer-lab-cshl

plinkQC:Genotype Quality Control with 'PLINK'

Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study.

Maintained by Hannah Meyer. Last updated 3 years ago.

6.4 match 58 stars 6.75 score 49 scripts

bioc

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.

snp geneticvariability qualitycontrol microarray

3.9 match 17 stars 10.50 score 396 scripts 5 dependents

spflanagan

fsthet:Fst-Heterozygosity Smoothed Quantiles

A program to generate smoothed quantiles for the Fst-heterozygosity distribution. Designed for use with large numbers of loci (e.g., genome-wide SNPs). The best case for analyzing the Fst-heterozygosity distribution is when many populations (>10) have been sampled. See Flanagan & Jones (2017) <doi:10.1093/jhered/esx048>.

Maintained by Sarah P. Flanagan. Last updated 7 years ago.

11.4 match 3.42 score 29 scripts

rqtl

qtl2:Quantitative Trait Locus Mapping in Experimental Crosses

Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.

Maintained by Karl W Broman. Last updated 8 days ago.

cpp

4.0 match 34 stars 9.48 score 1.1k scripts 5 dependents

emmanuelparadis

pegas:Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Maintained by Emmanuel Paradis. Last updated 1 years ago.

4.8 match 7.53 score 576 scripts 18 dependents

evolecolgroup

tidypopgen:Tidy Population Genetics

We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs).

Maintained by Andrea Manica. Last updated 3 days ago.

openblas zlib cpp openmp

5.6 match 4 stars 5.83 score 8 scripts

eppicenter

moire:Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

A Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation of individual level multiplicity of infection, within host relatedness, and population allele frequencies from polyallelic genetic data.

Maintained by Maxwell Murphy. Last updated 4 months ago.

genomics malaria mcmc cpp openmp

5.1 match 7 stars 5.14 score 22 scripts

bioc

GenVisR:Genomic Visualizations in R

Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Maintained by Zachary Skidmore. Last updated 5 months ago.

infrastructure datarepresentation classification dnaseq

2.5 match 215 stars 9.87 score 76 scripts

mjanuario

evolved:Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.

Maintained by Matheus Januario. Last updated 1 months ago.

3.3 match 3 stars 6.73 score 23 scripts

ice4prince

mixIndependR:Genetics and Independence Testing of Mixed Genetic Panels

Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.

Maintained by Bing Song. Last updated 4 years ago.

4.3 match 2 stars 4.48 score 8 scripts

migurke

GenoPop:Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files

Tools for efficient processing of large, whole genome genotype data sets in variant call format (VCF). It includes several functions to calculate commonly used population genomic metrics and a method for reference panel free genotype imputation, which is described in the preprint Gurke & Mayer (2024) <doi:10.22541/au.172515591.10119928/v1>.

Maintained by Marie Gurke. Last updated 4 months ago.

5.3 match 3.00 score 6 scripts

kenhanscombe

ukbtools:Manipulate and Explore UK Biobank Data

A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.

Maintained by Ken Hanscombe. Last updated 2 years ago.

biobank kcl-sgu uk-biobank ukb

2.3 match 101 stars 6.78 score 118 scripts

vsousa

poolHelper:Simulates Pooled Sequencing Genetic Data

Simulates pooled sequencing data under a variety of conditions. Also allows for the evaluation of the average absolute difference between allele frequencies computed from genotypes and those computed from pooled data. Carvalho et al., (2022) <doi:10.1101/2023.01.20.524733>.

Maintained by João Carvalho. Last updated 2 years ago.

3.5 match 4.18 score 3 scripts 1 dependents

bioc

midasHLA:R package for immunogenomics data handling and association analysis

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

Maintained by Maciej Migdał. Last updated 5 months ago.

cellbiology genetics statisticalmethod

3.0 match 4.30 score 3 scripts

jangraffelman

HardyWeinberg:Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.

Maintained by Jan Graffelman. Last updated 11 months ago.

cpp

2.0 match 6.30 score 167 scripts 4 dependents

thijsjanzen

GenomeAdmixR:Simulate Admixture of Genomes

Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.

Maintained by Thijs Janzen. Last updated 1 years ago.

cpp

2.3 match 5 stars 5.24 score 14 scripts

piyalkarum

rCNV:Detect Copy Number Variants from SNPs Data

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

Maintained by Piyal Karunarathne. Last updated 12 days ago.

cnv-analysis copy-number-variation gene-duplication genetics genomics landscape-genetics snps cpp

1.8 match 6 stars 4.26 score 4 scripts

ryan-graebner

GeneticSubsetter:Identify Favorable Subsets of Germplasm Collections

Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Maintained by Ryan C. Graebner. Last updated 8 years ago.

2.8 match 2.20 score 16 scripts

nmartinkova

diemr:Diagnostic Index Expectation Maximisation in R

Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.

Maintained by Natalia Martinkova. Last updated 2 months ago.

1.8 match 3.26 score 1 scripts

bioc

BubbleTree:BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

CNV analysis in groups of tumor samples.

Maintained by Todd Creasy. Last updated 5 months ago.

copynumbervariation software sequencing coverage

1.3 match 3.95 score 15 scripts

bioc

PureCN:Copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Maintained by Markus Riester. Last updated 2 months ago.

copynumbervariation software sequencing variantannotation variantdetection coverage immunooncology bioconductor-package cell-free-dna copy-number loh tumor-heterogeneity tumor-mutational-burden tumor-purity

0.5 match 132 stars 9.72 score 40 scripts

bioc

TitanCNA:Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Maintained by Gavin Ha. Last updated 5 months ago.

sequencing wholegenome dnaseq exomeseq statisticalmethod copynumbervariation hiddenmarkovmodel genetics genomicvariation immunooncology 10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity

0.5 match 96 stars 8.47 score 68 scripts

cran

EQUIVNONINF:Testing for Equivalence and Noninferiority

Making available in R the complete set of programs accompanying S. Wellek's (2010) monograph ''Testing Statistical Hypotheses of Equivalence and Noninferiority. Second Edition'' (Chapman&Hall/CRC).

Maintained by Stefan Wellek. Last updated 4 years ago.

3.2 match 1.30 score

bioc

tLOH:Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

Maintained by Michelle Webb. Last updated 5 months ago.

copynumbervariation transcription snp geneexpression transcriptomics

0.8 match 3 stars 4.48 score 4 scripts

bioc

VegaMC:VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Maintained by Sandro Morganella. Last updated 5 months ago.

acgh copynumbervariation

0.5 match 3.60 score 1 scripts

bioc

CNViz:Copy Number Visualization

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

Maintained by Rebecca Greenblatt. Last updated 5 months ago.

visualization copynumbervariation sequencing dnaseq

0.5 match 3.30 score 1 scripts

henrikbengtsson

calmate:Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.

Maintained by Henrik Bengtsson. Last updated 3 years ago.

acgh copynumbervariants snp microarray onechannel twochannel genetics

0.5 match 1 stars 2.70 score 6 scripts