Files in j-a-thia/genomalicious
A smorgasbord of R functions for population genomic analyses
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DESCRIPTION
DEV.R
LICENSE
NAMESPACE
PROJ_genomalicious.Rproj
R/.Rhistory
R/DT2Mat_freqs.R
R/DT2Mat_genos.R
R/DT2RADdata.R
R/DT2fasta.R
R/adegenet_DT2genX.R
R/align_many_genes_aa.R
R/align_many_genes_dna.R
R/align_plot_aa.R
R/align_plot_dna.R
R/allele_counts.R
R/allele_freq_corr_windows.R
R/allele_freqs_DT.R
R/allele_uniq_DT.R
R/amino_acid_names.R
R/annotDT2exonList.R
R/assembly_correct_gaps.R
R/bayescan_inputs_pools.R
R/bed2featuretab.R
R/circle_cutter.R
R/circularity_test.R
R/codonDT2genome.R
R/da2DT.R
R/dadi_inputs.R
R/dapc_fit.R
R/dapc_infer.R
R/dapc_plot.R
R/data_FreqsMat.R
R/data_Genos.R
R/data_PoolFreqs.R
R/data_PoolInfo.R
R/dna2codonDT.R
R/family_sim_compare.R
R/family_sim_genos.R
R/family_sim_qtl.R
R/fasta2DT.R
R/filter_depth.R
R/filter_maf.R
R/filter_missing_loci.R
R/filter_missing_units.R
R/filter_space_loci.R
R/filter_supporting_reads.R
R/filter_unlink.R
R/fstat_calc.R
R/gene_map_plot.R
R/genomalicious.R
R/genos2freqs.R
R/genos2indAlleles.R
R/genoscore_converter.R
R/het_calc.R
R/kmeans_join_DT.R
R/locus_overlap.R
R/miss_plot_heatmap.R
R/miss_plot_hist.R
R/mitoGbk2DT.R
R/mitogenome_seq_repos.R
R/mrbayes_input.R
R/normalise_patterson.R
R/outflank_input_freqs.R
R/outflank_mod_fst_correct.R
R/outflank_mod_fst_nocorrect.R
R/pairwiseMat2DT.R
R/pca2DT.R
R/pca_genos.R
R/pca_plot.R
R/pcoa_freqs.R
R/pcoa_plot.R
R/polyrad_DT2RADdata.R
R/poolfstat_DT2Fst.R
R/poolfstat_DT2pooldata.R
R/poolne_estim_boot_pi.R
R/poolne_estim_input.R
R/poolne_estim_output.R
R/replace_miss_genos.R
R/vcf2DT.R
README.md
archived/20220921/He_freqs.R
archived/20220921/fstWC_boot.R
archived/20220921/fstWC_freqs.R
archived/20220921/fstWC_genos.R
archived/20220921/fstWC_perm.R
archived/20220921/fstWC_varcomps.R
archived/20230104/adegenet_DT2genind.R
archived/20230104/adegenet_DT2genlight.R
archived/20230104/dadi_inputs_freqs.R
archived/20230104/dadi_inputs_genos.R
archived/20230104/fst_calc.R
archived/20230104/poolfstat_DT2pooldata.R
archived/20230104/poolfstat_pooldata2DT.R
data/data_FreqsMat.RData
data/data_Genos.RData
data/data_PoolFreqs.RData
data/data_PoolInfo.RData
deleted_scripts/vcf2DT_20191215_flipVersion.R
development/align_plot_aa.R
development/family_data_2.R
development/fst_plot.R
development/fstat_calc.R
development/fstat_subfun.R
development/fstat_varcomps.R
development/het_calc_backup_full.R
development/miss_plot_heatmap_v2.R
development/rda_fit.R
inst/doc/GenomaliciousTuts_1_Basics.R
inst/doc/GenomaliciousTuts_1_Basics.Rmd
inst/doc/GenomaliciousTuts_1_Basics.html
inst/extdata/data_Bcocosensis_mito_annots.bed
inst/extdata/data_Bcocosensis_mito_features.csv
inst/extdata/data_Bcocosensis_mitogenome.gbk
inst/extdata/data_COI_aa.fasta
inst/extdata/data_COI_dna.fasta
inst/extdata/data_Pop1_Dep.txt
inst/extdata/data_Pop1_Input.txt
inst/extdata/data_Pop1_Loci.txt
inst/extdata/data_Pop1_Ref.txt
inst/extdata/data_Pop1_res_ne_untruncated.out
inst/extdata/data_Pop1_summary_ne_eps.out
inst/extdata/data_Pop1_summary_pi.out
inst/extdata/data_Pop2_Dep.txt
inst/extdata/data_Pop2_Input.txt
inst/extdata/data_Pop2_Loci.txt
inst/extdata/data_Pop2_Ref.txt
inst/extdata/data_Pop2_res_ne_untruncated.out
inst/extdata/data_Pop2_summary_ne_eps.out
inst/extdata/data_Pop2_summary_pi.out
inst/extdata/data_Pop3_Dep.txt
inst/extdata/data_Pop3_Input.txt
inst/extdata/data_Pop3_Loci.txt
inst/extdata/data_Pop3_Ref.txt
inst/extdata/data_Pop3_res_ne_untruncated.out
inst/extdata/data_Pop3_summary_ne_eps.out
inst/extdata/data_Pop3_summary_pi.out
inst/extdata/data_Pop4_Dep.txt
inst/extdata/data_Pop4_Input.txt
inst/extdata/data_Pop4_Loci.txt
inst/extdata/data_Pop4_Ref.txt
inst/extdata/data_Pop4_res_ne_untruncated.out
inst/extdata/data_Pop4_summary_ne_eps.out
inst/extdata/data_Pop4_summary_pi.out
inst/extdata/data_indseq.vcf
inst/extdata/data_poolseq.vcf
inst/extdata/fsc2_sim_radseq_1_1.gen
man/DT2Mat_freqs.Rd
man/DT2Mat_genos.Rd
man/DT2RADdata.Rd
man/DT2fasta.Rd
man/adegenet_DT2genX.Rd
man/align_many_genes_aa.Rd
man/align_many_genes_dna.Rd
man/align_plot_aa.Rd
man/align_plot_dna.Rd
man/allele_counts.Rd
man/allele_freq_corr_windows.Rd
man/allele_freqs_DT.Rd
man/allele_uniq_DT.Rd
man/amino_acid_names.Rd
man/annotDT2exonList.Rd
man/assembly_correct_gaps.Rd
man/bayescan_inputs_pools.Rd
man/bed2featuretab.Rd
man/circle_cutter.Rd
man/circularity_test.Rd
man/codonDT2genome.Rd
man/da2DT.Rd
man/dadi_inputs.Rd
man/dapc_fit.Rd
man/dapc_infer.Rd
man/dapc_plot.Rd
man/data_FreqsMat.Rd
man/data_Genos.Rd
man/data_PoolFreqs.Rd
man/data_PoolInfo.Rd
man/dna2codonDT.Rd
man/family_sim_compare.Rd
man/family_sim_genos.Rd
man/family_sim_qtl.Rd
man/fasta2DT.Rd
man/filter_depth.Rd
man/filter_maf.Rd
man/filter_missing_loci.Rd
man/filter_missing_units.Rd
man/filter_space_loci.Rd
man/filter_supporting_reads.Rd
man/filter_unlink.Rd
man/fstat_calc.Rd
man/fstat_varcomps.Rd
man/gene_map_plot.Rd
man/genomalicious.Rd
man/genos2freqs.Rd
man/genos2indAlleles.Rd
man/genoscore_converter.Rd
man/het_calc.Rd
man/kmeans_join_DT.Rd
man/locus_overlap.Rd
man/miss_plot_heatmap.Rd
man/miss_plot_hist.Rd
man/mitoGbk2DT.Rd
man/mitogenome_seq_repos.Rd
man/mrbayes_input.Rd
man/normalise_patterson.Rd
man/outflank_input_freqs.Rd
man/outflank_mod_fst_correct.Rd
man/outflank_mod_fst_nocorrect.Rd
man/pairwiseMat2DT.Rd
man/pca2DT.Rd
man/pca_genos.Rd
man/pca_plot.Rd
man/pcoa_freqs.Rd
man/pcoa_plot.Rd
man/polyrad_DT2RADdata.Rd
man/poolfstat_DT2Fst.Rd
man/poolfstat_DT2pooldata.Rd
man/poolne_estim_boot_pi.Rd
man/poolne_estim_input.Rd
man/poolne_estim_output.Rd
man/replace_miss_genos.Rd
man/vcf2DT.Rd
vignettes/GenomaliciousTuts_01_Basics.Rmd
vignettes/GenomaliciousTuts_01_Basics.html
vignettes/GenomaliciousTuts_01_Basics.pdf
vignettes/GenomaliciousTuts_02_Quality.Rmd
vignettes/GenomaliciousTuts_02_Quality.html
vignettes/GenomaliciousTuts_02_Quality.pdf
vignettes/GenomaliciousTuts_03_Pop_structure.Rmd
vignettes/GenomaliciousTuts_03_Pop_structure.html
vignettes/GenomaliciousTuts_03_Pop_structure.pdf
