├── .gitignore ├── 01. Prepare TPM table.ipynb ├── 02. Calculate triad category.ipynb ├── 03. Classify genes by movment.ipynb ├── 04. Synthetic wheat calculate TPMs.ipynb ├── 05. Cumulative expression.ipynb ├── 06. Documentation of gene annotation.ipynb ├── 07. FAQ.ipynb ├── PaperFigures ├── Transcriptome Paper. Figure 2.ipynb └── percentage_of_triads_asigned_per_tissue.csv ├── README.md └── scripts ├── KaKs ├── kaks_chinesespring_UPLOAD.R ├── kaks_developmentset_UPLOAD.R ├── kaks_nonsyntenictriads_chinesespring_UPLOAD.R └── kaks_nonsyntenictriads_development_UPLOAD.R ├── MADSII_root └── blast_MADSII_root_module61.sh ├── TEs ├── TE_Family_Comparison_10-80-10_Movement_UPLOAD.R ├── calculate_sliding_windows_TEs.r ├── get_average_length_of_TEs_and_distance_to_ATG.r ├── plot_final_TE_density_graphs.r ├── retro_presenceabsence_subsetting_analysis_dominancecategories_with1500_UPLOAD.R └── retro_presenceabsence_subsetting_analysis_movementcategories_with1500_UPLOAD.R ├── TFBS ├── IWGSCv1.0_UTR.HC_1500bp_upstream_FIMO.sh ├── analyse_TF_motif_categories_1500bp.r ├── create_FIMO_unique_hits_tables_1500_slurm.sh ├── generate_TF_motif_groupings_1500bp.r └── generate_unique_TF_motifs_hits_1500bp.r ├── Tissue_differential_expression ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_anther.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_awns.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_embryo.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_endosperm.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_blade.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_sheath.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_glumes.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_hard.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_milk.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_internode.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_blades_excl_flag.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_ligule.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_sheaths_excl_flag.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_peduncle.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_root_apical_meristem.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_seedling_aerial_tissues.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_apical_meristem.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_axis.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spike.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spikelets.R ├── 1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_stigma_ovary.R ├── 2_filter_DE_padj0.05.R └── 3_summarise_DE_intermediate_tissues.R ├── WGCNA_network_construction ├── 1_WGCNA_combine_studies_filter_normalise_cluster_abiotic.R ├── 1_WGCNA_combine_studies_filter_normalise_cluster_disease.R ├── 1_WGCNA_combine_studies_filter_normalise_cluster_grain.R ├── 1_WGCNA_combine_studies_filter_normalise_cluster_leaf.R ├── 1_WGCNA_combine_studies_filter_normalise_cluster_root.R ├── 1_WGCNA_combine_studies_filter_normalise_cluster_spike.R ├── 2_WGCNA_cluster_thresholding_abiotic.R ├── 2_WGCNA_cluster_thresholding_disease.R ├── 2_WGCNA_cluster_thresholding_grain.R ├── 2_WGCNA_cluster_thresholding_leaf.R ├── 2_WGCNA_cluster_thresholding_root.R ├── 2_WGCNA_cluster_thresholding_spike.R ├── 3_WGCNA_cluster_co-expression_abiotic.R ├── 3_WGCNA_cluster_co-expression_disease.R ├── 3_WGCNA_cluster_co-expression_grain.R ├── 3_WGCNA_cluster_co-expression_leaf.R ├── 3_WGCNA_cluster_co-expression_root.R └── 3_WGCNA_cluster_co-expression_spike.R ├── compare_tissue_modules └── compare_modules.R ├── genome_of_origin_effect └── hclust_ABD_UPLOAD.r ├── hub_genes ├── find_hub_genes_abiotic.R └── find_hub_genes_disease.R ├── nullitetra ├── 1_plot_nullitetra_heatmap.R ├── 2_get_expression_nullitetra_1_1_1_triads.R ├── 3_add_dominance_category_to_1_1_1_triads.R └── 4_boxplot_1_1_1_triads_A_vs_D_vs_D_and_dominance_final_1tpm_threshold.R ├── same_similar_divergent_homoeolog_expression ├── 1_calculate_distance_between_homoeologs_all_tissues.R └── 2_plot_graphs_distance_all_tissues_triads_for_manuscript.R └── stress_correlations ├── module_trait_relationships_padj_abiotic.R └── module_trait_relationships_padj_disease_merge_same_stress.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/.gitignore -------------------------------------------------------------------------------- /01. Prepare TPM table.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/01. Prepare TPM table.ipynb -------------------------------------------------------------------------------- /02. Calculate triad category.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/02. Calculate triad category.ipynb -------------------------------------------------------------------------------- /03. Classify genes by movment.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/03. Classify genes by movment.ipynb -------------------------------------------------------------------------------- /04. Synthetic wheat calculate TPMs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/04. Synthetic wheat calculate TPMs.ipynb -------------------------------------------------------------------------------- /05. Cumulative expression.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/05. Cumulative expression.ipynb -------------------------------------------------------------------------------- /06. Documentation of gene annotation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/06. Documentation of gene annotation.ipynb -------------------------------------------------------------------------------- /07. FAQ.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/07. FAQ.ipynb -------------------------------------------------------------------------------- /PaperFigures/Transcriptome Paper. Figure 2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/PaperFigures/Transcriptome Paper. Figure 2.ipynb -------------------------------------------------------------------------------- /PaperFigures/percentage_of_triads_asigned_per_tissue.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/PaperFigures/percentage_of_triads_asigned_per_tissue.csv -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/README.md -------------------------------------------------------------------------------- /scripts/KaKs/kaks_chinesespring_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/KaKs/kaks_chinesespring_UPLOAD.R -------------------------------------------------------------------------------- /scripts/KaKs/kaks_developmentset_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/KaKs/kaks_developmentset_UPLOAD.R -------------------------------------------------------------------------------- /scripts/KaKs/kaks_nonsyntenictriads_chinesespring_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/KaKs/kaks_nonsyntenictriads_chinesespring_UPLOAD.R -------------------------------------------------------------------------------- /scripts/KaKs/kaks_nonsyntenictriads_development_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/KaKs/kaks_nonsyntenictriads_development_UPLOAD.R -------------------------------------------------------------------------------- /scripts/MADSII_root/blast_MADSII_root_module61.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/MADSII_root/blast_MADSII_root_module61.sh -------------------------------------------------------------------------------- /scripts/TEs/TE_Family_Comparison_10-80-10_Movement_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/TE_Family_Comparison_10-80-10_Movement_UPLOAD.R -------------------------------------------------------------------------------- /scripts/TEs/calculate_sliding_windows_TEs.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/calculate_sliding_windows_TEs.r -------------------------------------------------------------------------------- /scripts/TEs/get_average_length_of_TEs_and_distance_to_ATG.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/get_average_length_of_TEs_and_distance_to_ATG.r -------------------------------------------------------------------------------- /scripts/TEs/plot_final_TE_density_graphs.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/plot_final_TE_density_graphs.r -------------------------------------------------------------------------------- /scripts/TEs/retro_presenceabsence_subsetting_analysis_dominancecategories_with1500_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/retro_presenceabsence_subsetting_analysis_dominancecategories_with1500_UPLOAD.R -------------------------------------------------------------------------------- /scripts/TEs/retro_presenceabsence_subsetting_analysis_movementcategories_with1500_UPLOAD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TEs/retro_presenceabsence_subsetting_analysis_movementcategories_with1500_UPLOAD.R -------------------------------------------------------------------------------- /scripts/TFBS/IWGSCv1.0_UTR.HC_1500bp_upstream_FIMO.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TFBS/IWGSCv1.0_UTR.HC_1500bp_upstream_FIMO.sh -------------------------------------------------------------------------------- /scripts/TFBS/analyse_TF_motif_categories_1500bp.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TFBS/analyse_TF_motif_categories_1500bp.r -------------------------------------------------------------------------------- /scripts/TFBS/create_FIMO_unique_hits_tables_1500_slurm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TFBS/create_FIMO_unique_hits_tables_1500_slurm.sh -------------------------------------------------------------------------------- /scripts/TFBS/generate_TF_motif_groupings_1500bp.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TFBS/generate_TF_motif_groupings_1500bp.r -------------------------------------------------------------------------------- /scripts/TFBS/generate_unique_TF_motifs_hits_1500bp.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/TFBS/generate_unique_TF_motifs_hits_1500bp.r -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_anther.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_anther.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_awns.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_awns.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_embryo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_embryo.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_endosperm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_endosperm.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_blade.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_blade.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_sheath.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_flag_leaf_sheath.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_glumes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_glumes.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_hard.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_hard.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_milk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_grain_milk.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_internode.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_internode.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_blades_excl_flag.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_blades_excl_flag.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_ligule.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_ligule.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_sheaths_excl_flag.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_leaf_sheaths_excl_flag.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_peduncle.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_peduncle.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_root_apical_meristem.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_root_apical_meristem.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_seedling_aerial_tissues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_seedling_aerial_tissues.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_apical_meristem.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_apical_meristem.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_axis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_shoot_axis.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spike.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spike.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spikelets.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_spikelets.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_stigma_ovary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/1_DE_intermediate_tissues_script_for_cluster_one_tissue_at_a_time_stigma_ovary.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/2_filter_DE_padj0.05.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/2_filter_DE_padj0.05.R -------------------------------------------------------------------------------- /scripts/Tissue_differential_expression/3_summarise_DE_intermediate_tissues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/Tissue_differential_expression/3_summarise_DE_intermediate_tissues.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_abiotic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_abiotic.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_disease.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_disease.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_grain.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_grain.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_leaf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_leaf.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_root.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_root.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_spike.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/1_WGCNA_combine_studies_filter_normalise_cluster_spike.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_abiotic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_abiotic.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_disease.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_disease.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_grain.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_grain.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_leaf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_leaf.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_root.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_root.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_spike.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/2_WGCNA_cluster_thresholding_spike.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_abiotic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_abiotic.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_disease.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_disease.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_grain.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_grain.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_leaf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_leaf.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_root.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_root.R -------------------------------------------------------------------------------- /scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_spike.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/WGCNA_network_construction/3_WGCNA_cluster_co-expression_spike.R -------------------------------------------------------------------------------- /scripts/compare_tissue_modules/compare_modules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/compare_tissue_modules/compare_modules.R -------------------------------------------------------------------------------- /scripts/genome_of_origin_effect/hclust_ABD_UPLOAD.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/genome_of_origin_effect/hclust_ABD_UPLOAD.r -------------------------------------------------------------------------------- /scripts/hub_genes/find_hub_genes_abiotic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/hub_genes/find_hub_genes_abiotic.R -------------------------------------------------------------------------------- /scripts/hub_genes/find_hub_genes_disease.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/hub_genes/find_hub_genes_disease.R -------------------------------------------------------------------------------- /scripts/nullitetra/1_plot_nullitetra_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/nullitetra/1_plot_nullitetra_heatmap.R -------------------------------------------------------------------------------- /scripts/nullitetra/2_get_expression_nullitetra_1_1_1_triads.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/nullitetra/2_get_expression_nullitetra_1_1_1_triads.R -------------------------------------------------------------------------------- /scripts/nullitetra/3_add_dominance_category_to_1_1_1_triads.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/nullitetra/3_add_dominance_category_to_1_1_1_triads.R -------------------------------------------------------------------------------- /scripts/nullitetra/4_boxplot_1_1_1_triads_A_vs_D_vs_D_and_dominance_final_1tpm_threshold.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/nullitetra/4_boxplot_1_1_1_triads_A_vs_D_vs_D_and_dominance_final_1tpm_threshold.R -------------------------------------------------------------------------------- /scripts/same_similar_divergent_homoeolog_expression/1_calculate_distance_between_homoeologs_all_tissues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/same_similar_divergent_homoeolog_expression/1_calculate_distance_between_homoeologs_all_tissues.R -------------------------------------------------------------------------------- /scripts/same_similar_divergent_homoeolog_expression/2_plot_graphs_distance_all_tissues_triads_for_manuscript.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/same_similar_divergent_homoeolog_expression/2_plot_graphs_distance_all_tissues_triads_for_manuscript.R -------------------------------------------------------------------------------- /scripts/stress_correlations/module_trait_relationships_padj_abiotic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/stress_correlations/module_trait_relationships_padj_abiotic.R -------------------------------------------------------------------------------- /scripts/stress_correlations/module_trait_relationships_padj_disease_merge_same_stress.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Uauy-Lab/WheatHomoeologExpression/HEAD/scripts/stress_correlations/module_trait_relationships_padj_disease_merge_same_stress.R --------------------------------------------------------------------------------