Exploratory Analysis of Genetic and Genomic Data

accessors | Accessors for adegenet objects |

adegenet.package | The adegenet package |

AICc | snapclust's corrected Akaike Information Criterion (AICc) |

AIC.snapclust | snapclust's Akaike Information Criterion (AIC) |

ascore | Compute and optimize a-score for Discriminant Analysis of... |

as.genlight | Conversion to class "genlight" |

as-methods | Converting genind/genpop objects to other classes |

as.SNPbin | Conversion to class "SNPbin" |

auxil | Auxiliary functions for adegenet |

BIC.snapclust | snapclust's Bayesian Information Criterion (BIC) |

chooseCN | Function to choose a connection network |

colorplot | Represents a cloud of points with colors |

compoplot | Genotype composition plot |

coords.monmonier | Returns original points in results paths of an object of... |

dapc | Discriminant Analysis of Principal Components (DAPC) |

dapcGraphics | Graphics for Discriminant Analysis of Principal Components... |

dapcIllus | Simulated data illustrating the DAPC |

df2genind | Convert a data.frame of allele data to a genind object. |

dist.genpop | Genetic distances between populations |

doc_C_routines | Internal C routines |

eHGDP | Extended HGDP-CEPH dataset |

export_to_mvmapper | Export analysis for mvmapper visualisation |

fasta2DNAbin | Read large DNA alignments into R |

fasta2genlight | Extract Single Nucleotide Polymorphism (SNPs) from alignments |

find.clusters | find.cluster: cluster identification using successive K-means |

gengraph | Genetic transitive graphs |

genind | adegenet formal class (S4) for individual genotypes |

genind2df | Convert a genind object to a data.frame. |

genind2genpop | Conversion from a genind to a genpop object |

genlight | Formal class "genlight" |

genpop | adegenet formal class (S4) for allele counts in populations |

glAux | Auxiliary functions for genlight objects |

glPca | Principal Component Analysis for genlight objects |

glPlot | Plotting genlight objects |

glSim | Simulation of simple genlight objects |

H3N2 | Seasonal influenza (H3N2) HA segment data |

haploGen | Simulation of genealogies of haplotypes |

hierarchy-methods | Access and manipulate the population hierarchy for genind or... |

Hs | Expected heterozygosity (Hs) |

Hs.test | Test differences in expected heterozygosity (Hs) |

HWE | Hardy-Weinberg Equilibrium test for multilocus data |

hybridize | Function hybridize takes two genind in inputs and generates... |

hybridtoy | Toy hybrid dataset |

import2genind | Importing data from several softwares to a genind object |

inbreeding | Likelihood-based estimation of inbreeding |

isPoly | Assess polymorphism in genind/genpop objects |

KIC | snapclust's Kullback Information Criterion (KIC) |

loadingplot | Represents a cloud of points with colors |

makefreq | Compute allelic frequencies |

microbov | Microsatellites genotypes of 15 cattle breeds |

minorAllele | Compute minor allele frequency |

monmonier | Boundary detection using Monmonier algorithm |

mutations | Identify mutations between DNA sequences |

nancycats | Microsatellites genotypes of 237 cats from 17 colonies of... |

new.genind | genind constructor |

new.genpop | genpop constructor |

old2new | Convert objects with obsolete classes into new objects |

pairDist | Pairwise distance plots |

population-methods | Manipulate the population factor of genind objects. |

propShared | Compute proportion of shared alleles |

propTyped | Compute the proportion of typed elements |

read.fstat | Reading data from Fstat |

read.genepop | Reading data from Genepop |

read.genetix | Reading data from GENETIX |

read.PLINK | Reading PLINK Single Nucleotide Polymorphism data |

read.snp | Reading Single Nucleotide Polymorphism data |

read.structure | Reading data from STRUCTURE |

repool | Pool several genotypes into a single dataset |

rupica | Microsatellites genotypes of 335 chamois (Rupicapra... |

scaleGen | Compute scaled allele frequencies |

selpopsize | Select genotypes of well-represented populations |

seploc | Separate data per locus |

seppop | Separate genotypes per population |

seqTrack | SeqTrack algorithm for reconstructing genealogies |

sequences | Importing data from an alignement of sequences to a genind... |

servers | Web servers for adegenet |

showmekittens | When you need a break... |

sim2pop | Simulated genotypes of two georeferenced populations |

snapclust | Maximum-likelihood genetic clustering using EM algorithm |

snapclust.choose.k | Choose the number of clusters for snapclust |

SNPbin | Formal class "SNPbin" |

snpposi | Analyse the position of polymorphic sites |

snpzip | Identification of structural SNPs |

spca | Spatial principal component analysis |

spcaIllus | Simulated data illustrating the sPCA |

spca_randtest | Monte Carlo test for sPCA |

spca.rtests | Global and local tests |

strata-methods | Access and manipulate the population strata for genind or... |

tab | Access allele counts or frequencies |

truenames | Restore true labels of an object |

virClasses | Virtual classes for adegenet |

web | Functions to access online resources for adegenet |

xvalDapc | Cross-validation for Discriminant Analysis of Principal... |

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