├── Dockerfile ├── README.md ├── RNAseq_workflow.pptx ├── docs ├── 404.html ├── _config.yml ├── _includes │ ├── head.html │ ├── navigation.html │ ├── scripts.html │ ├── search-results.html │ ├── search.html │ ├── sidebar.html │ └── styles.html ├── _layouts │ ├── default.html │ └── page.html ├── _sass │ ├── milligram.scss │ ├── prism.scss │ └── variables.scss ├── alignment.md ├── alnpractical.md ├── assets │ ├── css │ │ └── docs.scss │ ├── images │ │ ├── close.svg │ │ ├── favicon.ico │ │ └── menu.svg │ └── js │ │ ├── database.js │ │ ├── lunar.min.js │ │ ├── mobile-navigation.js │ │ ├── prism.min.js │ │ ├── search.js │ │ └── zepto.min.js ├── challenge.md ├── course_data.md ├── differential_expression.md ├── expdesign.md ├── fastq.md ├── functional_analysis.md ├── gbrowser.md ├── images │ ├── 800px-Mapping_Reads.png │ ├── A549_0_1_1_screen.png │ ├── A549_0_1_1_screen_1.png │ ├── A549_0_1_1_screen_2.png │ ├── Double-stranded_RNA.gif │ ├── GO_example_graph.png │ ├── GO_logo.png │ ├── GO_tool_input1.png │ ├── GO_tool_interface.png │ ├── GO_tool_result1.png │ ├── GO_tool_results_ensembl.png │ ├── GO_tool_results_symbols.png │ ├── PCA.png │ ├── PCA_star.png │ ├── README.md │ ├── RNAseq_dispersion.png │ ├── RNAseq_workflow.png │ ├── adapter_removed.png │ ├── bad_fastqc.png │ ├── batch_effect_pca.png │ ├── confounded_design.png │ ├── encode1.png │ ├── encode2.png │ ├── enrichr_interface.png │ ├── enrichr_interface2.png │ ├── enrichr_paper1.jpg │ ├── enrichr_results_all.png │ ├── enrichr_results_bar.png │ ├── enrichr_results_clustergram.png │ ├── enrichr_results_network.png │ ├── enrichr_results_table.png │ ├── ensembl_1.png │ ├── ensembl_2.png │ ├── ensembl_3.png │ ├── exp_design.jpg │ ├── fasta_format.png │ ├── fastq_format.png │ ├── fastqc.png │ ├── fastqc_small_rnas.png │ ├── gencode_1.png │ ├── gencode_2.png │ ├── gsea_downloads.png │ ├── gsea_explained.gif │ ├── gsea_interface.png │ ├── gsea_load_files.png │ ├── gsea_msig_banner.png │ ├── gsea_msig_sets.png │ ├── gsea_paper.jpg │ ├── gsea_parameters_commented.png │ ├── gsea_phenotypes.png │ ├── gsea_presentation.png │ ├── gsea_report_process.png │ ├── gsea_results_details1.png │ ├── gsea_results_details2.png │ ├── gsea_results_details3.png │ ├── gsea_results_index.png │ ├── gsea_results_index_commented.png │ ├── gsea_results_stats.png │ ├── gsea_run_parameters.png │ ├── gsea_txt.gif │ ├── illumina1.png │ ├── illumina2.png │ ├── illumina3.png │ ├── illumina4.png │ ├── illumina5.png │ ├── illumina6.png │ ├── index_kmer.png │ ├── kegg_hsa05218.png │ ├── mappers_timeline.jpeg │ ├── multiplexing.jpg │ ├── multiqc.png │ ├── non_confounded_design.png │ ├── phred_quality.png │ ├── qualimap1.png │ ├── qualimap2.png │ ├── qualimap3.png │ ├── qualimap4.png │ ├── rnaseq2g_UI.png │ ├── sample_distance_heatmap.png │ ├── sample_distance_heatmap_star.png │ ├── size_dist_small.png │ ├── stranded_protocol.png │ ├── stranded_vs_unstranded.jpg │ ├── tileshop.jpeg │ ├── transcription.jpg │ ├── ucsc1.png │ ├── ucsc10.png │ ├── ucsc2.png │ ├── ucsc3.png │ ├── ucsc4.png │ ├── ucsc5.png │ ├── ucsc6.png │ ├── ucsc7.png │ ├── ucsc8.png │ └── ucsc9.png ├── index.md ├── intro.md ├── library.md ├── linux_containers.md ├── multiqc.md ├── pics │ ├── lcozzuto.jpg │ ├── ponomarenko.jpg │ └── sbonnin.jpg ├── precomp_res │ ├── A549_0_1_fastq_screen.tar.gz │ └── full_data.tar.gz ├── qc.md ├── repositories.md ├── resources.md ├── salmon.md └── workflow.md ├── full_data ├── counts_salmon │ ├── A549_0_1 │ │ └── quant.sf.gz │ ├── A549_0_2 │ │ └── quant.sf.gz │ ├── A549_0_3 │ │ └── quant.sf.gz │ ├── A549_25_1 │ │ └── quant.sf.gz │ ├── A549_25_2 │ │ └── quant.sf.gz │ └── A549_25_3 │ │ └── quant.sf.gz └── counts_star │ ├── A549_0_1ReadsPerGene.out.tab.gz │ ├── A549_0_2ReadsPerGene.out.tab.gz │ ├── A549_0_3ReadsPerGene.out.tab.gz │ ├── A549_25_1ReadsPerGene.out.tab.gz │ ├── A549_25_2ReadsPerGene.out.tab.gz │ └── A549_25_3ReadsPerGene.out.tab.gz └── resources.md /Dockerfile: 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