# README file whitefish_translocation_pipeline.txt: Demultiplexing, trimming, and aligning ddRADseq and epiRADseq data. STACKS pipeline. Data preparation for genomic analyses epiRADseq_pipeline.md : preparing epiRADseq data # R scripts # Morphological analyses morphology_01_geometric_morphometrics.R morphology_02_allometry_correction.R morphology_03_linear_trait_analysis.R # Stable isotope analysis stable_isotope_01_metrics.R # Genomic analyses genomics_01_batch_effect_epiRAD_ddRAD.R genomics_02_inbreeding_plink_plot.R genomics_02_relatedness_plink.R genomics_03_PCA_SNPRelate.R genomics_04_RDA.R genomics_05_Allele_frequency.R # Epigenetic analyses epigenomics_01_batch_effect_loci.R epigenomics_02_edgeR_analysis.R epigenomics_03_PCA.R epigenomics_04_RDA.R RDA_morphology_genomics_epigenomics.R # Genotype quality assessment genotype_checks_heterozygous_miscall_rate_script.R genotype_checks_rarefied_allelic_richness_script.R