Files in momeara/CalCEN

CalCEN: Estimate Co-Expression Networks

R/biogrid.R R/define_runs.R R/download_expression_data.R R/estimate_expression.R R/load_parameters.R R/prepare_reference_genome.R R/util.R R/validate_estimated_expression.R README.md inst/hpc/run_estimate_expression.R man/date_code.Rd man/download_expression_data.Rd man/estimate_expression.Rd man/get_sra_connection.Rd man/load_parameters.Rd man/prepare_reference_genome.Rd man/read_biogrid_tab2.Rd man/retrieve_sra_runs.Rd man/submit_estimate_expression_slurm.Rd man/validate_downloaded_runs.Rd man/validate_estimated_runs.Rd parameters.R vignettes/CalCEN/scripts/10_analyze_go_term_prediction.R vignettes/CalCEN/scripts/10_plot_go_pred.R vignettes/CalCEN/scripts/11_hit_intersection.R vignettes/CalCEN/scripts/12_annotate_apms.R vignettes/CalCEN/scripts/13_SILAC_HSP90_perturbation_correation.R vignettes/CalCEN/scripts/13_SILAC_clusters.R vignettes/CalCEN/scripts/13_annotate_apms2.R vignettes/CalCEN/scripts/13_silac_correlation.R vignettes/CalCEN/scripts/14_annotate_apms3.R vignettes/CalCEN/scripts/14_silac_clusters_parallel.R vignettes/CalCEN/scripts/15_silac_vs_coexp.R vignettes/CalCEN/scripts/15_stress_granule_gene_prediction.R vignettes/CalCEN/scripts/16_SILAC_significant_hsp90_correlation.R vignettes/CalCEN/scripts/17_gene_summary.R vignettes/CalCEN/scripts/18_gather_publication_data.R vignettes/CalCEN/scripts/1_define_runs.R vignettes/CalCEN/scripts/1_gather_APMS_data.R vignettes/CalCEN/scripts/1_gather_CGD_data.R vignettes/CalCEN/scripts/1_gather_YGD.R vignettes/CalCEN/scripts/1_gather_biogrid_data.R vignettes/CalCEN/scripts/1_gather_cococonet.R vignettes/CalCEN/scripts/1_gather_human_stress_granule_members.R vignettes/CalCEN/scripts/1_gather_interesting_genes.R vignettes/CalCEN/scripts/1_gather_sac_stress_granules.R vignettes/CalCEN/scripts/1_gather_sgd_interactions.R vignettes/CalCEN/scripts/1_gather_silac_Ca-Sc-Sp_data.R vignettes/CalCEN/scripts/1_gather_silac_HSP90_depletion_data.R vignettes/CalCEN/scripts/1_gather_yeastnet_data.R vignettes/CalCEN/scripts/2_define_genes.R vignettes/CalCEN/scripts/2_download_runs.R vignettes/CalCEN/scripts/2_propagate_go_annotations.R vignettes/CalCEN/scripts/3_reference_genome.R vignettes/CalCEN/scripts/4_build_crossmap_network.R vignettes/CalCEN/scripts/4_sequence_similarity.R vignettes/CalCEN/scripts/4_stress_granule_othology.R vignettes/CalCEN/scripts/4_submit_estimate_expression.R vignettes/CalCEN/scripts/5.1.1_gather_estimated_expression.R vignettes/CalCEN/scripts/5.1.2_gather_estimated_expression_meta.R vignettes/CalCEN/scripts/6.1.1_rna_seq_quality_control.R vignettes/CalCEN/scripts/6.1.2_build_coexp_network.R vignettes/CalCEN/scripts/6.1.3_p_compare_correlation_measures.R vignettes/CalCEN/scripts/6.1.4_build_ca_coexp_data_ablation_network.R vignettes/CalCEN/scripts/6_build_CoCoCoNet_network.R vignettes/CalCEN/scripts/6_build_co_annotation_network.R vignettes/CalCEN/scripts/6_build_ppi_network.R vignettes/CalCEN/scripts/6_build_sac_ppi_network.R vignettes/CalCEN/scripts/6_build_sequence_similarity_network.R vignettes/CalCEN/scripts/6_build_silac_network.R vignettes/CalCEN/scripts/6_build_yeast_net_network.R vignettes/CalCEN/scripts/7.2_embed_ca_coexp_net.R vignettes/CalCEN/scripts/7_extend_TAPinteractors_cytoscape.R vignettes/CalCEN/scripts/7_plot_coexp_network.R vignettes/CalCEN/scripts/7_plot_distribution_of_expression_levels.R vignettes/CalCEN/scripts/7_plot_percent_reads_mapped_for_runs_in_studies.R vignettes/CalCEN/scripts/7_plot_silac_change_in_intensities.R vignettes/CalCEN/scripts/7_plot_silac_gain_vs_loss.R vignettes/CalCEN/scripts/7_plot_silac_intensities_heatmap.R vignettes/CalCEN/scripts/7_plot_silac_sum_abs_log_fc.R vignettes/CalCEN/scripts/7_silac_clusters_under_hsp90_depletion.R vignettes/CalCEN/scripts/7_silac_genetic_vs_pharmacological.R vignettes/CalCEN/scripts/8_top_co_expressed_genes.R vignettes/CalCEN/scripts/9.1_predicted_go_terms.R vignettes/CalCEN/scripts/9_go_term_prediction.R vignettes/CalCEN/scripts/9_network_overlap.R vignettes/CalCEN/scripts/alluvial.R vignettes/CalCEN/scripts/annotate.R vignettes/CalCEN/scripts/apms_prey_id_map.R vignettes/CalCEN/scripts/embed_network.R vignettes/CalCEN/scripts/estimate_expression.R vignettes/CalCEN/scripts/evaluate_network_gba.R vignettes/CalCEN/scripts/gene_report.R vignettes/CalCEN/scripts/parameters_template.R vignettes/CalCEN/scripts/parse_biogrid.R vignettes/CalCEN/scripts/run_estimate_expression.R vignettes/CalCEN/scripts/seriation_heatmap.R vignettes/CalCEN/scripts/uniprot_to_cgd_id.R vignettes/CryptoCEN/scripts/1_gather_fungidb_data.R vignettes/CryptoCEN/scripts/2.1_define_runs.R vignettes/CryptoCEN/scripts/2.2_reference_genome.R vignettes/CryptoCEN/scripts/2.3_download_runs.R vignettes/CryptoCEN/scripts/2.4_submit_estimated_expression.R vignettes/CryptoCEN/scripts/3.1_gather_biogrid_data.R