stackr/NAMESPACE at master · caitiecollins/stackr · GitHub

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# Generated by roxygen2: do not edit by hand

export(blacklist_loci)
export(build_stacks_workflow_dir)
export(dart2df_genind_plink)
export(data_pruning)
export(diagnostic_maf)
export(erase_genotypes)
export(filter_fis)
export(filter_genotype_likelihood)
export(filter_het)
export(filter_id_whitelist)
export(filter_individual)
export(filter_loci_blacklist)
export(filter_maf)
export(filter_population)
export(filter_snp_number)
export(find_duplicate_genome)
export(genomic_converter)
export(genotypes_summary)
export(haplo2colony)
export(individuals2strata)
export(make_tfam)
export(missing_visualization)
export(plink_ibm)
export(plot_boxplot_coverage)
export(plot_boxplot_diversity)
export(plot_boxplot_genotype_likelihood)
export(plot_coverage_imbalance_diagnostic)
export(plot_density_distribution_coverage)
export(plot_density_distribution_genotype_likelihood)
export(plot_density_distribution_het)
export(plot_density_distribution_maf)
export(plot_distribution_diversity)
export(plot_snp_number_loci)
export(plot_snp_position_read)
export(population_map)
export(read_long_tidy_wide)
export(ref_alt_alleles)
export(run_cstacks)
export(run_sstacks)
export(stackr_imputations_module)
export(summary_coverage)
export(summary_genotype_likelihood)
export(summary_haplotypes)
export(summary_hapstats)
export(summary_phistats)
export(summary_stats_pop)
export(summary_stats_vcf_tidy)
export(sumstats_prep)
export(table_low_coverage_summary)
export(tidy_genepop)
export(tidy_genomic_data)
export(tidy_stacks_haplotypes_vcf)
export(vcf2betadiv)
export(vcf2dadi)
export(vcf2genepop)
export(vcf2genind)
export(vcf2genlight)
export(vcf2gtypes)
export(vcf2hierfstat)
export(vcf2plink)
export(vcf2structure)
export(vcf_imputation)
export(vcf_strata)
export(whitelist_loci)
export(whitelist_loci_snp)
export(whitelist_snp_vcf)
export(write_betadiv)
export(write_genepop)
export(write_genind)
export(write_genlight)
export(write_gtypes)
export(write_hierfstat)
export(write_plink)
export(write_structure)
export(write_vcf)
import(adegenet)
import(dplyr)
import(ggplot2)
import(lazyeval)
import(parallel)
import(readr)
import(reshape2)
import(stringi)
import(tidyr)
import(utils)
importFrom(amap,Dist)
importFrom(ape,pcoa)
importFrom(data.table,as.data.table)
importFrom(data.table,fread)
importFrom(data.table,melt.data.table)
importFrom(dplyr,as_data_frame)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(methods,new)
importFrom(parallel,mclapply)
importFrom(plyr,colwise)
importFrom(purrr,detect_index)
importFrom(purrr,discard)
importFrom(purrr,flatten)
importFrom(purrr,flatten_chr)
importFrom(purrr,invoke)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(readr,write_tsv)
importFrom(stats,chisq.test)
importFrom(stats,dist)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,var)
importFrom(stringdist,stringdist)
importFrom(stringi,stri_paste)
importFrom(stringi,stri_replace_all_fixed)
importFrom(stringi,stri_split_fixed)
importFrom(tidyr,gather)
importFrom(tidyr,separate)
importFrom(utils,combn)
importFrom(utils,count.fields)
importFrom(utils,packageVersion)
importFrom(utils,write.table)