├── README.md ├── _config.yml ├── activities ├── day1_polls.md ├── day2_polls.md ├── day3_polls.md ├── day4_polls.md └── practice_exercise.md ├── assets ├── css │ └── style.scss └── images │ └── dna-sequence-1600x800.jpg ├── data ├── DGE_workshop_annotations.RData ├── Mov10_full_meta.txt ├── annotations_ahb.csv ├── multiqc_report_rnaseq.html ├── multiqc_report_rnaseq.html.zip ├── raw_counts_mouseKO.csv └── tx2gene_grch38_ens94.txt ├── exercises ├── DGE_analysis_exercises answer_key.md ├── DGE_analysis_exercises.md └── refresher_answers.R ├── homework ├── DGE_assignment_1.R ├── DGE_assignment_1_answer_key.R ├── DGE_assignment_2.R ├── DGE_assignment_2_answer_key.R ├── DGE_assignment_3.R └── exp_design_table.xlsx ├── img ├── Create_RStudio_Project.gif ├── Differential_expression.png ├── MA_plot.png ├── NB_model_formula.png ├── PCA_2sample_genes.png ├── PCA_2sample_influence.png ├── PCA_2sample_rotate.png ├── PCA_2sample_variation1.png ├── PCA_2sample_variation2.png ├── PCA_2sample_variation3.png ├── PCA_salmon.png ├── PCA_samples.png ├── bad_dispersion1.png ├── bad_dispersion2.png ├── batch_effect.png ├── batch_effect_pca.png ├── cluster_summary.png ├── cnetplot-2_salmon.png ├── cnetplot1_salmon.png ├── confounded_batch.png ├── confounded_design.png ├── dataset.png ├── de_norm_counts_var.png ├── de_replicates_img2.png ├── de_theory.png ├── de_variation.png ├── de_workflow_salmon.png ├── de_workflow_salmon_deseq1.png ├── de_workflow_salmon_deseq2.png ├── de_workflow_salmon_normalization.png ├── de_workflow_salmon_qc.png ├── degPatterns_figure.png ├── degReport_clusters2.png ├── degpattern_figure.tiff ├── deseq2_shrunken_lfc.png ├── deseq2_workflow_separate.png ├── deseq2_workflow_separate_dis.png ├── deseq2_workflow_separate_fit.png ├── deseq2_workflow_separate_sf.png ├── deseq2_workflow_separate_shr.png ├── deseq_counts_distribution.png ├── deseq_counts_overview.png ├── deseq_dispersion1.png ├── deseq_dispersion2.png ├── deseq_mean_variance2.png ├── deseq_median_of_ratios.png ├── deseq_nb.png ├── deseq_obj1.png ├── deseq_obj2.png ├── emapplot_salmon.png ├── example_PCA_cage.png ├── example_PCA_sex.png ├── example_PCA_strain.png ├── example_PCA_treatmentPC1.png ├── example_PCA_treatmentPC3.png ├── example_metadata.png ├── exercise_dispersion.png ├── gProfiler.png ├── gene_filtering.png ├── genemania.png ├── go_freq.png ├── go_heirarchy.jpg ├── go_proportions.png ├── go_proportions_table3.png ├── gseaKEGGresults.png ├── gsea_kegg_hsa03008.png ├── gsea_kegg_hsa03040.png ├── gsea_overview.png ├── gsea_theory.png ├── heatmap_example.png ├── heatmap_sleuth.png ├── hsa03008.pathview.png ├── hsa03040.pathview.png ├── hsa05222.png ├── hypergeo.png ├── illumina_sequencing_process.png ├── indep_filt_scatterplus.png ├── library_prep.png ├── lrt_formula.png ├── lrt_time_nodiff.png ├── lrt_time_yesdiff.png ├── maplot_unshrunken.png ├── melt_wide_to_long_format.png ├── meta_example.png ├── metadata_batch.png ├── mov10-model.png ├── mov10_isoform_expression.png ├── mov10_test_table.png ├── mov10oe_dotplot.png ├── non_confounded_design.png ├── normalization_methods_composition.png ├── normalization_methods_depth.png ├── normalization_methods_length.png ├── orgdb_annotation_databases.png ├── paired_end_reads.png ├── pathway_analysis.png ├── pca_sleuth.png ├── pheatmap_aug2020.png ├── pheatmap_salmon.png ├── plotCounts_ggrepel_salmon.png ├── plotDispersion_salmon.png ├── plot_density_filtered.png ├── plot_density_unfiltered.png ├── quant_screenshot.png ├── replicates.png ├── revigo_download_link.png ├── revigo_input.png ├── revigo_treemap.png ├── rlog_transformation_new.png ├── salmon.png ├── sample_qc.png ├── settingup.png ├── sigOE_heatmap.png ├── sig_genes_gather_salmon.png ├── sleuth_abund_h5.png ├── sleuth_bootstraps1.png ├── sleuth_bootstraps2.png ├── sleuth_cor_heatmap.png ├── sleuth_formula1.png ├── sleuth_formula2.png ├── sleuth_mov10_results.png ├── sleuth_pca_loadings.png ├── sleuth_pca_variance.png ├── sleuth_tech_var.png ├── sleuth_workflow.png ├── sleuth_workflow1.png ├── sleuth_workflow2_updated.png ├── spia_plot.png ├── topgen_plot.png ├── topgen_plot_salmon.png ├── volcano_plot_1_salmon.png ├── volcano_plot_2_salmon.png ├── workflow-salmon-DGE-alt2.png └── workflow-salmon-sleuth.png ├── lectures ├── Intro_to_workshop_CFAR.pdf ├── Intro_to_workshop_all.pdf ├── Workshop_wrapup.pdf ├── Workshop_wrapup_CFAR.pdf ├── Workshop_wrapup_all.pdf ├── Workshop_wrapup_dfhcc.pdf ├── workshop_intro_slides.pdf └── workshop_wrapup_slides.pdf ├── lessons ├── 01a_RNAseq_processing_workflow.md ├── 01b_DGE_setup_and_overview.md ├── 01c_RNAseq_count_distribution.md ├── 02_DGE_count_normalization.md ├── 03_DGE_QC_analysis.md ├── 04a_design_formulas.md ├── 04b_DGE_DESeq2_analysis.md ├── 05a_hypothesis_testing.md ├── 05b_wald_test_results.md ├── 05c_summarizing_results.md ├── 06_DGE_visualizing_results.md ├── 07_DGE_summarizing_workflow.md ├── 08a_DGE_LRT_results.md ├── 08b_time_course_analyses.md ├── 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