Files in thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

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DESCRIPTION

LICENSE.md

NAMESPACE

NEWS.md R/allele_frequencies.R R/bayescan.R R/betas_estimator.R R/calibrate_alleles.R R/clean.R R/dart.R R/detect_all_missing.R R/detect_allele_problems.R R/detect_biallelic_markers.R R/detect_biallelic_problems.R R/detect_duplicate_genomes.R R/detect_genomic_format.R R/detect_het_outliers.R R/detect_microsatellites.R R/detect_mixed_genomes.R R/detect_paralogs.R R/detect_ref_genome.R R/diagnostic_ma.R R/erase_genotypes.R R/filter_blacklist_genotypes.R R/filter_common_markers.R R/filter_coverage.R R/filter_dart_reproducibility.R R/filter_fis.R R/filter_genotyping.R R/filter_het.R R/filter_hwe.R R/filter_individuals.R R/filter_ld.R R/filter_ma.R R/filter_monomorphic.R R/filter_rad.R R/filter_snp_number.R R/filter_snp_position_read.R R/filter_whitelist.R R/fstat.R R/gds.R R/genepop.R R/genind.R R/genlight.R R/genomic_converter.R R/global_variables.R R/gsi_sim.R R/gtypes.R R/haplotype_reconstruction.R R/ibdg_fh.R R/pi.R R/plink.R R/private_alleles.R R/private_haplotypes.R R/radiator.R R/radiator_deprecated_functions.R R/radiator_dots.R R/radiator_import_from.R R/radiator_pkg_install.R R/radiator_tidy.R R/read_rad.R R/sex_markers.R R/snprelate.R R/strata.R R/summary_rad.R R/utils.R R/vcf.R R/visualization.R R/write_arlequin.R R/write_betadiv.R R/write_colony.R R/write_dadi.R R/write_faststructure.R R/write_fineradstructure.R R/write_genepopedit.R R/write_hapmap.R R/write_hzar.R R/write_ldna.R R/write_maverick.R R/write_pcadapt.R R/write_related.R R/write_rubias.R R/write_stockr.R R/write_structure.R README.Rmd README.md

_pkgdown.yml

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inst/CITATION

man/.Rapp.history

man/Exposition_pipe_operator.Rd man/allele_count.Rd man/allele_frequencies.Rd man/assign_defaults.Rd man/bayescan_one.Rd man/betas_estimator.Rd man/blacklist_hw.Rd man/boxplot_stats.Rd man/calibrate_alleles.Rd man/change_pop_names.Rd man/check_args_class.Rd man/check_dart.Rd man/check_header_source_vcf.Rd man/check_pop_levels.Rd man/clean_dart_colnames.Rd man/clean_dart_locus.Rd man/clean_ind_names.Rd man/clean_markers_names.Rd man/clean_pop_names.Rd man/compound_assignment_pipe_operator.Rd man/compute_maf.Rd man/count_monomorphic.Rd man/dart2gds.Rd man/data_info.Rd man/detect_all_missing.Rd man/detect_allele_problems.Rd man/detect_biallelic_markers.Rd man/detect_biallelic_problems.Rd man/detect_dart_format.Rd man/detect_duplicate_genomes.Rd man/detect_genomic_format.Rd man/detect_gt.Rd man/detect_het_outliers.Rd man/detect_microsatellites.Rd man/detect_mixed_genomes.Rd man/detect_paralogs.Rd man/detect_ref_genome.Rd man/diagnostic_maf.Rd man/distance2tibble.Rd man/distance_individuals.Rd man/erase_genotypes.Rd man/estimate_m.Rd man/extract_coverage.Rd man/extract_dart_target_id.Rd man/extract_data_source.Rd man/extract_dots.Rd man/extract_genotypes_metadata.Rd man/extract_individuals_metadata.Rd man/extract_individuals_vcf.Rd man/extract_info_vcf.Rd man/extract_markers_metadata.Rd man/filter_blacklist_genotypes.Rd man/filter_common_markers.Rd man/filter_coverage.Rd man/filter_dart_reproducibility.Rd man/filter_fis.Rd man/filter_genotyping.Rd man/filter_het.Rd man/filter_hwe.Rd man/filter_individuals.Rd man/filter_ld.Rd man/filter_ma.Rd man/filter_monomorphic.Rd man/filter_rad.Rd man/filter_snp_number.Rd man/filter_snp_position_read.Rd man/filter_whitelist.Rd man/folder_prefix.Rd man/folder_short.Rd man/gds2tidy.Rd man/generate_filename.Rd man/generate_folder.Rd man/generate_geno_freq_boundaries.Rd man/generate_gt_vcf_nuc.Rd man/generate_hzar.Rd man/generate_markers_metadata.Rd man/generate_squeleton_folders.Rd man/generate_stats.Rd man/generate_strata.Rd man/generate_whitelist.Rd man/genome_similarity.Rd man/genomic_converter.Rd man/gt2array.Rd man/gt_recoding.Rd man/haplotype_reconstruction.Rd man/hwe_analysis.Rd man/ibdg_fh.Rd man/import_dart.Rd man/ind_total_reads.Rd man/individual_het.Rd man/individuals2strata.Rd man/join_rad.Rd man/join_strata.Rd man/ld2df.Rd man/ld_boxplot.Rd man/ld_missing.Rd man/ld_pruning.Rd man/list_filters.Rd man/ma_one.Rd man/markers_fis.Rd man/markers_genotyped_helper.Rd man/markers_het.Rd man/merge_dart.Rd man/message_func_call.Rd man/minor_allele_stats.Rd man/missing_per_pop.Rd man/n.Rd man/not_common_markers.Rd man/parallel_core_opt.Rd man/parse_gds_metadata.Rd man/pi.Rd man/pi_pop.Rd man/pi_rad.Rd man/pipe.Rd man/plot_bayescan.Rd man/plot_boxplot_coverage.Rd man/plot_boxplot_diversity.Rd man/plot_coverage_imbalance_diagnostic.Rd man/plot_density_distribution_coverage.Rd man/plot_density_distribution_het.Rd man/plot_density_distribution_maf.Rd man/plot_distribution_diversity.Rd man/plot_het_outliers.Rd man/plot_snp_number_loci.Rd man/plot_snp_position_read.Rd man/plot_upset.Rd man/private_alleles.Rd man/private_haplotypes.Rd man/rad_long.Rd man/rad_wide.Rd man/radiator_common_arguments.Rd man/radiator_dots.Rd man/radiator_folder.Rd man/radiator_function_header.Rd man/radiator_future.Rd man/radiator_gds.Rd man/radiator_gds_skeleton.Rd man/radiator_packages_dep.Rd man/radiator_parameters.Rd man/radiator_pkg_install.Rd man/radiator_question.Rd man/radiator_results_message.Rd man/radiator_snakecase.Rd man/radiator_split_tibble.Rd man/radiator_tic.Rd man/radiator_toc.Rd man/read_blacklist_genotypes.Rd man/read_blacklist_id.Rd man/read_dart.Rd man/read_plink.Rd man/read_rad.Rd man/read_strata.Rd man/read_vcf.Rd man/read_whitelist.Rd man/remove_duplicates.Rd man/replace_by_na.Rd man/reset_filters.Rd man/run_bayescan.Rd man/separate_gt.Rd man/separate_markers.Rd man/sex_markers_plot.Rd man/sexy_markers.Rd man/simulate_genos_from_posterior.Rd man/split_tibble_rows.Rd 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man/write_hierfstat.Rd man/write_hzar.Rd man/write_ldna.Rd man/write_maverick.Rd man/write_pcadapt.Rd man/write_plink.Rd man/write_rad.Rd man/write_related.Rd man/write_rubias.Rd man/write_snprelate.Rd man/write_stockr.Rd man/write_structure.Rd man/write_vcf.Rd

radiator.Rproj

vignettes/.gitignore

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vignettes/get_started.R vignettes/get_started.Rmd

vignettes/get_started.html

vignettes/life_cycle.R vignettes/life_cycle.Rmd

vignettes/life_cycle.html

vignettes/rad_genomics_computer_setup.R vignettes/rad_genomics_computer_setup.Rmd

vignettes/rad_genomics_computer_setup.html

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thierrygosselin/radiator documentation built on April 25, 2024, 3:20 a.m.