adegenet formal class (S4) for individual genotypes
Auxiliary functions for adegenet
Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)
Simulation of genealogies of haplotypes
Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
Discriminant Analysis of Principal Components (DAPC)
Compute minor allele frequency
Test differences in expected heterozygosity (Hs)
Conversion from a genind to a genpop object
Likelihood-based estimation of inbreeding
Plotting genlight objects
Extended HGDP-CEPH dataset
Convert a data.frame of allele data to a genind object.
Simulation of simple genlight objects
Convert a genind object to a data.frame.
adegenet formal class (S4) for allele counts in populations
Access and manipulate the population hierarchy for genind or genlight objects.
Hardy-Weinberg Equilibrium test for multilocus data
Read large DNA alignments into R
Boundary detection using Monmonier algorithm
Reading Single Nucleotide Polymorphism data
The adegenet package
Manipulate the population factor of genind objects.
Identify mutations between DNA sequences
Pairwise distance plots
Principal Component Analysis for genlight objects
Represents a cloud of points with colors
Function to choose a connection network
Formal class "genlight"
Importing data from several softwares to a genind object
Formal class "SNPbin"
Compute the proportion of typed elements
Simulated data illustrating the sPCA
Compute proportion of shared alleles
Convert objects with obsolete classes into new objects
Access allele counts or frequencies
Web servers for adegenet
Converting genind/genpop objects to other classes
Select genotypes of well-represented populations
Seasonal influenza (H3N2) HA segment data
Conversion to class "genlight"
genind constructor
Assess polymorphism in genind/genpop objects
Reading data from STRUCTURE
Represents a cloud of points with colors
Compute allelic frequencies
Reading PLINK Single Nucleotide Polymorphism data
Analyse the position of polymorphic sites
Restore true labels of an object
Pool several genotypes into a single dataset
Simulated genotypes of two georeferenced populations
Microsatellites genotypes of 15 cattle breeds
genpop constructor
Function hybridize takes two genind in inputs
and generates hybrids individuals having one parent
in both objects.
Separate data per locus
genlight auxiliary functions
Auxiliary functions for genlight objects
Global and local tests
Access and manipulate the population strata for genind or genlight objects.
Reading data from Fstat
Genetic distances between populations
Importing data from an alignement of sequences to a genind object
Virtual classes for adegenet
Spatial principal component analysis
Simulated data illustrating the DAPC
find.cluster: cluster identification using successive K-means
Reading data from GENETIX
SeqTrack algorithm for reconstructing genealogies
Conversion to class "SNPbin"
Accessors for adegenet objects
Functions to access online resources for adegenet
Expected heterozygosity (Hs)
Graphics for Discriminant Analysis of Principal Components (DAPC)
Reading data from Genepop
Returns original points in results paths of an object of class 'monmonier'
Cross-validation for Discriminant Analysis of Principal Components (DAPC)
Genetic transitive graphs
Extract Single Nucleotide Polymorphism (SNPs) from alignments
Compute scaled allele frequencies
Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the
Bauges mountains (France)
Separate genotypes per population