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02-F0_homozygosity_files/figure-html		02-F0_homozygosity_files/figure-html
02-cross-refs_files/figure-html		02-cross-refs_files/figure-html
03-2-F2_recombination_files/figure-html		03-2-F2_recombination_files/figure-html
03-F2_recombination_files/figure-html		03-F2_recombination_files/figure-html
04-1-Phenotype_exploration_files/figure-html		04-1-Phenotype_exploration_files/figure-html
05-GWLS_results_files/figure-html		05-GWLS_results_files/figure-html
Inverse_normalise_by_microscope_files/figure-html		Inverse_normalise_by_microscope_files/figure-html
Period_intercept_with_AU_files/figure-html		Period_intercept_with_AU_files/figure-html
Period_intercept_with_DB_files/figure-html		Period_intercept_with_DB_files/figure-html
Reporter_as_covariate_files/figure-html		Reporter_as_covariate_files/figure-html
plots		plots
source		source
.DS_Store		.DS_Store
.gitignore		.gitignore
01-Data_processing_with_Snakemake.Rmd		01-Data_processing_with_Snakemake.Rmd
01-Data_processing_with_Snakemake.html		01-Data_processing_with_Snakemake.html
01-background.qmd		01-background.qmd
02-F0_and_F1_homozygosity.Rmd		02-F0_and_F1_homozygosity.Rmd
02-F0_and_F1_homozygosity.html		02-F0_and_F1_homozygosity.html
02-F0_homozygosity.Rmd		02-F0_homozygosity.Rmd
02-F0_homozygosity.html		02-F0_homozygosity.html
02-phenotypes.qmd		02-phenotypes.qmd
03-1-F2_recombination_all_sites.Rmd		03-1-F2_recombination_all_sites.Rmd
03-1-F2_recombination_all_sites.html		03-1-F2_recombination_all_sites.html
03-2-F2_recombination.Rmd		03-2-F2_recombination.Rmd
03-2-F2_recombination.rmarkdown		03-2-F2_recombination.rmarkdown
03-2-F2_recombination_no_repeat_sites.Rmd		03-2-F2_recombination_no_repeat_sites.Rmd
03-3-F2_recombination.Rmd		03-3-F2_recombination.Rmd
03-3-F2_recombination_no_repeat_reads.Rmd		03-3-F2_recombination_no_repeat_reads.Rmd
03-4-F2_recombination_no_repeat_reads_or_pers_hets.Rmd		03-4-F2_recombination_no_repeat_reads_or_pers_hets.Rmd
03-5-F2_recombination_no_repeat_reads_or_pers_hets_filtered_for_read_count_and_cab_prop.Rmd		03-5-F2_recombination_no_repeat_reads_or_pers_hets_filtered_for_read_count_and_cab_prop.Rmd
03-F0-homozygosity.qmd		03-F0-homozygosity.qmd
03-F2_recombination.Rmd		03-F2_recombination.Rmd
04-1-Phenotype_exploration.Rmd		04-1-Phenotype_exploration.Rmd
04-2-Test_GWAS_code.Rmd		04-2-Test_GWAS_code.Rmd
04-F1-heterozygosity.qmd		04-F1-heterozygosity.qmd
05-F2-genotyping.qmd		05-F2-genotyping.qmd
05-GWLS_results.Rmd		05-GWLS_results.Rmd
06-GWAS.qmd		06-GWAS.qmd
06-method_testing.Rmd		06-method_testing.Rmd
06_check_permutations.Rmd		06_check_permutations.Rmd
07-process_phenotypes_for_Ewan.Rmd		07-process_phenotypes_for_Ewan.Rmd
07-references.Rmd		07-references.Rmd
07-references.qmd		07-references.qmd
08-Annotations.Rmd		08-Annotations.Rmd
20221121_Ali_human_genome.qmd		20221121_Ali_human_genome.qmd
404.html		404.html
Add_covariates_to_GWLS.Rmd		Add_covariates_to_GWLS.Rmd
Add_reporter_geno_to_pheno_file.Rmd		Add_reporter_geno_to_pheno_file.Rmd
Exploration_of_hits_PSM.Rmd		Exploration_of_hits_PSM.Rmd
Exploration_of_hits_intercept.Rmd		Exploration_of_hits_intercept.Rmd
F1_homozygosity.Rmd		F1_homozygosity.Rmd
Hit_exploration_for_Ewan.Rmd		Hit_exploration_for_Ewan.Rmd
Inverse_normalise_by_microscope.Rmd		Inverse_normalise_by_microscope.Rmd
Microscope-adjusted_pheno.Rmd		Microscope-adjusted_pheno.Rmd
New_GWAS_call.Rmd		New_GWAS_call.Rmd
Period_intercept_subtr_diff.Rmd		Period_intercept_subtr_diff.Rmd
Period_intercept_with_AU.Rmd		Period_intercept_with_AU.Rmd
Period_intercept_with_DB.Rmd		Period_intercept_with_DB.Rmd
Reporter_as_covariate.Rmd		Reporter_as_covariate.Rmd
Reporter_concordance.Rmd		Reporter_concordance.Rmd
Tom_HMM_walkthrough.Rmd		Tom_HMM_walkthrough.Rmd
_04-citations.Rmd		_04-citations.Rmd
_05-GridLMM_example.Rmd		_05-GridLMM_example.Rmd
_05-blocks.Rmd		_05-blocks.Rmd
_06-share.Rmd		_06-share.Rmd
_bookdown.yml		_bookdown.yml
_common.R		_common.R
_output.yml		_output.yml
_quarto.yml		_quarto.yml
book.bib		book.bib
book.rds		book.rds
chicago-fullnote-bibliography.csl		chicago-fullnote-bibliography.csl
css.html		css.html
index.Rmd		index.Rmd
index.qmd		index.qmd
packages.bib		packages.bib
style.css		style.css
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