├── .DS_Store ├── README.md ├── _config.yml ├── assets ├── css │ └── style.scss └── images │ └── dna-sequence-1600x800.jpg ├── data ├── Mov10_full_meta.txt ├── counts.rpkm.csv ├── mouse_exp_design.csv └── normalized_counts.txt ├── homework ├── Intro_to_R_hw.md └── plotcounts.png ├── img ├── DESeq2_workflow.png ├── DGE_workflow_full.png ├── MA_plot.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_samples.png ├── README.md ├── RNAseqWorkflow.png ├── Rplot.png ├── Rplot01.png ├── Rstudio_interface.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_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_normalization.png ├── deseq_workflow_qc.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 ├── 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 ├── 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 ├── 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 ├── 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_clusters.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 ├── partition_variance.png ├── pathway_analysis.png ├── pca_500.png ├── pheatmap-1.png ├── plotCounts_ggrepel.png ├── plotDispersion.png ├── r_starting_how_it_should_like.png ├── revigo_input.png ├── revigo_output.png ├── rlog_transformation.png ├── rnaseq_full_workflow.png ├── rstudio_logo.png ├── sample_qc.png ├── scatter-plot1.png ├── scatter-plot2.png ├── scatter-plot3.png ├── scatter-plot4.png ├── scatter-plot5.png ├── script_editor.png ├── script_editor_output.png ├── sequencing_depth.png ├── settingup.png ├── setwd.png ├── sigOE_heatmap.png ├── sig_genes_melt.png ├── slide12_DGE.png ├── slide16+33_DGE.png ├── slide16+33_DGE_alt.png ├── slide16_DGE.png ├── slide5_DGE.png ├── teachin-team.png ├── tools_options.png ├── topgen_plot.png ├── unnamed-chunk-10-1.png ├── unnamed-chunk-11-1.png ├── unnamed-chunk-12-1.png ├── unnamed-chunk-13-1.png ├── unnamed-chunk-14-1.png ├── unnamed-chunk-15-1.png ├── var_in_reps.png ├── vector-index.png ├── vector1.png ├── vector2.png ├── vector3.png ├── vector4.png ├── vector5-logical.png ├── volcanoplot-1-labeled.png ├── volcanoplot-1.png ├── volcanoplot-1_new.png ├── volcanoplot-2.png ├── wald_test.png ├── wd_setup.png ├── why_R.png └── wrap_option.png ├── lectures ├── Intro_to_workshop.pdf ├── Intro_to_workshop_PQG.pdf ├── Workshop_wrapup.pdf └── Workshop_wrapup_PQG.pdf ├── lessons ├── B1_DGE_visualizing_results.md ├── basic_plots_in_r.md ├── functional_analysis_other_methods.md └── principal_component_analysis.md └── schedule ├── PQG_schedule.md ├── README.md └── files ├── PQG_2018 ├── Day2_refresher.R ├── animals.csv ├── de_script.R ├── functional_analysis.R └── intro-to-r.R ├── data_type_and_structures.txt ├── functions.txt ├── intro_r.R └── refresher.R /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hbctraining/Intro-to-R-with-DGE/HEAD/.DS_Store -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hbctraining/Intro-to-R-with-DGE/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- 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