$<-.gen_tbl             A $ method for 'gen_tibble' objects
arrange.gen_tbl         An arrange method for 'gen_tibble' objects
arrange.grouped_gen_tbl
                        An arrange method for grouped 'gen_tibble'
                        objects
augment.gt_dapc         Augment data with information from a gt_dapc
                        object
augment_gt_pca          Augment data with information from a gt_pca
                        object
augment_loci            Augment the loci table with information from a
                        analysis object
augment_loci_gt_pca     Augment the loci table with information from a
                        gt_pca object
augment_q_matrix        Augment data with information from a q_matrix
                        object
autoplot.gt_cluster_pca
                        Autoplots for 'gt_cluster_pca' objects
autoplot.gt_dapc        Autoplots for 'gt_dapc' objects
autoplot.qc_report_indiv
                        Autoplots for 'qc_report_indiv' objects
autoplot.qc_report_loci
                        Autoplots for 'qc_report_loci' objects
autoplot_gt_admix       Autoplots for 'gt_admix' objects
autoplot_gt_pca         Autoplots for 'gt_pca' objects
autoplot_gt_pcadapt     Autoplots for 'gt_pcadapt' objects
autoplot_q_matrix       Autoplots for 'q_matrix' objects
c.gt_admix              Combine method for gt_admix objects
cbind.gen_tbl           Combine a gen_tibble to a data.frame or tibble
                        by column
count_loci              Count the number of loci in a 'gen_tibble'
distruct_colours        Distruct colours
filter.gen_tbl          Tidyverse methods for gt objects
filter.grouped_gen_tbl
                        A filter method for grouped 'gen_tibble'
                        objects
filter_high_relatedness
                        Filter individuals based on a relationship
                        threshold
find_duplicated_loci    Find duplicates in the loci table
gen_tibble              Constructor for a 'gen_tibble'
get_p_matrix            Return a single P matrix from a 'gt_admix'
                        object
get_q_matrix            Return a single Q matrix from a 'gt_admix'
                        object
gt_add_sf               Add an simple feature geometry to a
                        'gen_tibble'
gt_admix_reorder_q      Reorder the q matrices based on the grouping
                        variable
gt_admixture            Run ADMIXTURE from R
gt_as_genind            Convert a 'gen_tibble' to a 'genind' object
                        from 'adegenet'
gt_as_genlight          Convert a 'gen_tibble' to a 'genlight' object
                        from 'adegenet'
gt_as_geno_lea          Convert a 'gentibble' to a .geno file for sNMF
                        from the LEA package
gt_as_hierfstat         Convert a 'gen_tibble' to a data.frame
                        compatible with 'hierfstat'
gt_as_plink             Export a 'gen_tibble' object to PLINK bed
                        format
gt_as_vcf               Convert a 'gen_tibble' to a VCF
gt_cluster_pca          Run K-clustering on principal components
gt_cluster_pca_best_k   Find the best number of clusters based on
                        principal components
gt_dapc                 Discriminant Analysis of Principal Components
                        for gen_tibble
gt_extract_f2           Compute and store blocked f2 statistics for
                        ADMIXTOOLS 2
gt_from_genlight        Convert a 'genlight' object from adegenet to a
                        'gen_tibble'
gt_get_file_names       Get the names of files storing the genotypes of
                        a 'gen_tibble'
gt_has_imputed          Checks if a 'gen_tibble' has been imputed
gt_impute_simple        Simple imputation based on allele frequencies
gt_impute_xgboost       Imputation based XGBoost
gt_load                 Load a gen_tibble
gt_order_loci           Order the loci table of a gen_tibble
gt_pca                  Principal Component Analysis for 'gen_tibble'
                        objects
gt_pca_autoSVD          PCA controlling for LD for 'gen_tibble' objects
gt_pca_partialSVD       PCA for 'gen_tibble' objects by partial SVD
gt_pca_randomSVD        PCA for 'gen_tibble' objects by randomized
                        partial SVD
gt_pcadapt              pcadapt analysis on a 'gen_tibble' object
gt_pseudohaploid        Set the ploidy of a 'gen_tibble' to include
                        pseudohaploids
gt_save                 Save a gen_tibble
gt_set_imputed          Sets a 'gen_tibble' to use imputed data
gt_snmf                 Run SNMF from R in tidypopgen
gt_update_backingfile   Update the backing matrix
gt_uses_imputed         Checks if a 'gen_tibble' uses imputed data
indiv_het_obs           Estimate individual observed heterozygosity
indiv_inbreeding        Individual inbreeding coefficient
indiv_missingness       Estimate individual missingness
indiv_ploidy            Return individual ploidy
is_loci_table_ordered   Test if the loci table is ordered
load_example_gt         Load example gen_tibble
loci_alt_freq           Estimate allele frequencies at each locus
loci_chromosomes        Get the chromosomes of loci in a 'gen_tibble'
loci_hwe                Test Hardy-Weinberg equilibrium at each locus
loci_ld_clump           Clump loci based on a Linkage Disequilibrium
                        threshold
loci_missingness        Estimate missingness at each locus
loci_names              Get the names of loci in a 'gen_tibble'
loci_pi                 Estimate nucleotide diversity (pi) at each
                        locus
loci_transitions        Find transitions
loci_transversions      Find transversions
mutate.gen_tbl          A mutate method for 'gen_tibble' objects
mutate.grouped_gen_tbl
                        A mutate method for grouped 'gen_tibble'
                        objects
nwise_pop_pbs           Compute the Population Branch Statistics for
                        each combination of populations
pairwise_allele_sharing
                        Compute the Pairwise Allele Sharing Matrix for
                        a 'gen_tibble' object
pairwise_grm            Compute the Genomic Relationship Matrix for a
                        'gen_tibble' object
pairwise_ibs            Compute the Identity by State Matrix for a
                        'gen_tibble' object
pairwise_king           Compute the KING-robust Matrix for a
                        'gen_tibble' object
pairwise_pop_fst        Compute pairwise population Fst
pop_fis                 Compute population specific FIS
pop_fst                 Compute population specific Fst
pop_global_stats        Compute basic population global statistics
pop_het_exp             Compute the population expected heterozygosity
pop_het_obs             Compute the population observed heterozygosity
pop_tajimas_d           Estimate Tajima's D for the whole genome
predict.gt_pca          Predict scores of a PCA
q_matrix                Convert a standard matrix to a 'q_matrix'
                        object
qc_report_indiv         Create a Quality Control report for individuals
qc_report_loci          Create a Quality Control report for loci
rbind.gen_tbl           Combine two gen_tibbles
rbind_dry_run           Generate a report of what would happen to each
                        SNP in a merge
read_q_files            Read and structure .Q files or existing
                        matrices as 'q_matrix' or 'gt_admix' objects.
scale_fill_distruct     Scale constructor using the distruct colours
select_loci             The 'select' verb for 'loci'
select_loci_if          The 'select_if' verb for 'loci'
show_genotypes          Show the genotypes of a 'gen_tibble'
show_loci               Show the loci information of a 'gen_tibble'
show_ploidy             Show the ploidy information of a 'gen_tibble'
snp_allele_sharing      Compute the Pairwise Allele Sharing Matrix for
                        a bigSNP object
snp_ibs                 Compute the Identity by State Matrix for a
                        bigSNP object
snp_king                Compute the KING-robust Matrix for a bigSNP
                        object
summary.gt_admix        Summary method for gt_admix objects
summary.rbind_report    Print a summary of a merge report
theme_distruct          A theme to match the output of distruct
tidy.gt_dapc            Tidy a 'gt_dapc' object
tidy.gt_pca             Tidy a 'gt_pca' object
tidy.q_matrix           Tidy a Q matrix
upset_plot              Draw an UpSet plot from a data frame of logical
                        columns
windows_indiv_roh       Detect runs of homozygosity using a
                        sliding-window approach
windows_nwise_pop_pbs   Compute the Population Branch Statistics over a
                        sliding window
windows_pairwise_pop_fst
                        Compute pairwise Fst for a sliding window
windows_pop_tajimas_d   Compute Tajima's D for a sliding window
windows_stats_generic   Estimate window statistics from per locus
                        estimates
