├── README.md ├── _config.yml ├── assets ├── css │ └── style.scss └── images │ └── dna-sequence-1600x800.jpg ├── data └── Mov10_full_meta.txt ├── exercises ├── DGE_analysis_exercises answer_key.md └── DGE_analysis_exercises.md ├── img ├── DESeq2_workflow.png ├── DESeq2_workflow_2018.png ├── DGE_workflow_full.png ├── MA_plot.png ├── Mov10oe_DEgenes_heatmap.png ├── NB_model_formula.png ├── NB_model_formula_betas.png ├── NB_model_formula_betas_example.png ├── NB_model_formula_betas_example2.png ├── NB_model_formula_betas_example3.png ├── Overview_DGE_workshop.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_example.png ├── PCA_example1.png ├── PCA_example2.png ├── PCA_example3.png ├── PCA_example4.png ├── PCA_example5.png ├── PCA_example6.png ├── PCA_example7.png ├── PCA_example8.png ├── PCA_samples.png ├── README.md ├── alignmentfree_workflow.png ├── alignmentfree_workflow2.png ├── available_annotations.png ├── bad_dispersion1.png ├── bad_dispersion2.jpeg ├── bad_dispersion2.png ├── bar-5-new.png ├── bar-5.png ├── bioconductor_logo.png ├── biomart_query.png ├── boxplot-1.png ├── cluster_summary.png ├── cnet.png ├── complete_wd_setup.png ├── console.png ├── counts_view.png ├── cran_packages.png ├── dataframe.png ├── dataset.png ├── de_norm_counts_var.png ├── de_replicates_img.png ├── de_theory.png ├── de_variation.png ├── deg_methods1.png ├── deg_methods2.png ├── deseq2_mean_vs_variance2.png ├── deseq2_shrunken_lfc.png ├── deseq2_shrunken_lfc2.png ├── deseq2_workflow_separate.png ├── deseq2_workflow_separate_2018.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_distribution_zoomed.png ├── deseq_counts_overview.png ├── deseq_dispersion1.png ├── deseq_dispersion2.png ├── deseq_mean_vs_variance.png ├── deseq_mean_vs_variance_dispersion.png ├── deseq_median_of_ratios.png ├── deseq_nb.png ├── deseq_obj1.png ├── deseq_obj2.png ├── deseq_workflow.png ├── deseq_workflow1.png ├── deseq_workflow_full.png ├── deseq_workflow_full_2018.png ├── deseq_workflow_normalization.png ├── deseq_workflow_normalization_2018.png ├── deseq_workflow_qc.png ├── deseq_workflow_qc_2018.png ├── diag-ontology-graph.gif ├── dotplot.png ├── drawings.pptx ├── ego2_example.png ├── enrich.png ├── ensembl_biomart.png ├── ensembl_human.png ├── ensembl_interface.png ├── ensembl_mov10_gene.png ├── ensembl_transcripts.png ├── environment.png ├── example_PCA_cage.png ├── example_PCA_sex.png ├── example_PCA_strain.png ├── example_PCA_treatmentPC1.png ├── example_PCA_treatmentPC3.png ├── example_metadata.png ├── factors.png ├── factors_both.png ├── factors_new.png ├── factors_sm.png ├── factors_sm_intact.png ├── foldchange_heatmap.png ├── gProfiler.png ├── gene_filtering.png ├── genemania.png ├── generic_complete_wd_setup.png ├── generic_rstudio_interface.png ├── generic_wd_setup.png ├── getwd.png ├── ggboxplot.png ├── gghist-1.png ├── gghist-2.png ├── ggplot_help.png ├── ggscatter-1.png ├── ggscatter-2.png ├── ggscatter-3.png ├── ggscatter-4.png ├── ggscatter-5.png ├── go_freq.png ├── go_heirarchy.jpg ├── go_proportions.png ├── go_proportions_table.png ├── go_proportions_table2.png ├── go_proportions_table3.png ├── gsea_theory.png ├── heatmap_example.png ├── hist-1.png ├── hsa03040.pathview.png ├── hsa05222.png ├── hypergeo.png ├── in-operator1-new.png ├── in-operator1.png ├── in-operator2.png ├── in-operator3.png ├── intro-to-galaxy--iclip.html ├── length_of_gene.png ├── list.png ├── logic.idx.png ├── lrt_time_nodiff.png ├── lrt_time_yesdiff.png ├── maplot_unshrunken.png ├── match1.png ├── match2.png ├── match3-reordered.png ├── match4-idx.png ├── matrix.png ├── melt_long_format.png ├── melt_wide_format.png ├── melt_wide_to_long_format.png ├── meta_example.png ├── meta_example2.png ├── metadata.png ├── metadata_view.png ├── mov10-model.png ├── mov10_bootstraps.png ├── mov10_clusters.png ├── mov10_isoform_expression.png ├── mov10_isoform_png.png ├── mov10_test_table.png ├── mov10oe1_cnet_plot.png ├── mov10oe_cnet_plot.png ├── mov10oe_cnetplot.png ├── mov10oe_cnetplot2.png ├── mov10oe_dotplot.png ├── mov10oe_enrichmap.png ├── mrna_to_reads.png ├── normalization_methods_composition.png ├── normalization_methods_depth.png ├── normalization_methods_length.png ├── orgdb_annotation_databases.png ├── partition_variance.png ├── pathway_analysis.png ├── pca_500.png ├── pca_with_PC1_line.png ├── pheatmap-1.png ├── plotCounts_ggrepel.png ├── plotDispersion.png ├── revigo_download_link.png ├── revigo_input.png ├── revigo_output.png ├── revigo_treemap.pdf ├── revigo_treemap.png ├── rlog_transformation.png ├── rnaseq_full_workflow.png ├── rstudio_pseudocounts.png ├── salmon_file.png ├── salmon_quasialignment.png ├── salmon_rstudio.png ├── sample_qc.png ├── scatter-plot1.png ├── scatter-plot2.png ├── scatter-plot3.png ├── scatter-plot4.png ├── scatter-plot5.png ├── sequencing_depth.png ├── settingup.png ├── sigOE_heatmap.png ├── sigOE_heatmap2.png ├── sig_genes_melt.png ├── sig_genes_melt2.png ├── sleuth_MA.png ├── sleuth_QQ.png ├── sleuth_abund_h5.png ├── sleuth_dir.png ├── sleuth_dispersion.png ├── sleuth_formula1.png ├── sleuth_formula2.png ├── sleuth_fullworkflow.png ├── sleuth_fullworkflow_new.png ├── sleuth_fullworkflow_new2.png ├── sleuth_heatmap.png ├── sleuth_mean-variance.png ├── sleuth_meta.png ├── sleuth_mov10_bootstraps.png ├── sleuth_mov10_bootstraps2.png ├── sleuth_mov10_density.png ├── sleuth_mov10_density_no_filter.png ├── sleuth_mov10_heatmap.png ├── sleuth_mov10_ma.png ├── sleuth_mov10_pca.png ├── sleuth_mov10_results.png ├── sleuth_object.png ├── sleuth_pca.png ├── sleuth_pca_loadings.png ├── sleuth_pca_variance.png ├── sleuth_plot_pca.png ├── sleuth_results.png ├── sleuth_scatter.png ├── sleuth_tech_var.png ├── sleuth_transcripts_heatmap.png ├── sleuth_volcano.png ├── sleuth_workflow.png ├── sleuth_workflow1.png ├── sleuth_workflow2.png ├── sleuth_workflow2_updated.png ├── sleuth_workflow3.png ├── slide12_DGE.png ├── slide16+33_DGE.png ├── slide16+33_DGE_alt.png ├── slide16_DGE.png ├── slide5_DGE.png ├── topgen_plot.png ├── var_in_reps.png ├── volcano_plot_new1.png ├── volcano_plot_new2.png └── wald_test.png ├── lessons ├── 01_DGE_setup_and_overview.md ├── 02_DGE_count_normalization.md ├── 03_DGE_QC_analysis.md ├── 04_DGE_DESeq2_analysis.md ├── 05_DGE_DESeq2_analysis2.md ├── 06_DGE_visualizing_results.md ├── 07_DGE_summarizing_workflow.md ├── 08_DGE_LRT.md ├── 09_functional_analysis.md ├── DGE_visualizing_results_archived.md ├── functional_analysis_other_methods.md ├── mov10_knockdown.md └── principal_component_analysis.md ├── schedule └── 1.5-day.md ├── slides ├── RNAseq-analysis-methods.pdf └── rnaseq_stats_qc.pdf └── test_folder └── example_folder.md /README.md: 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