├── .github └── workflows │ └── main.yml ├── .gitignore ├── Bad_RNASeq_Examples ├── Bias_GC_Content.jpeg ├── PBAT-base-composition.png ├── Positional sequence bias in random primed libraries.png ├── Technical_Duplication.png ├── biased_composition.png ├── fastqc_sequence_length_distribution_plot-2-1.png └── rseqc_inner_distance_plot-1.png ├── Dockerfile ├── LICENSE ├── README.md ├── _site.yml ├── assets ├── cover.png ├── end.png ├── favicon.ico ├── favicon.png ├── footer-lab.Rmd ├── footer-lab.html ├── footer-slide.Rmd ├── freepik.jpg ├── header-lab.Rmd ├── header-slide.Rmd ├── lab.css ├── landing.png ├── logo.svg ├── remark-latest.min.js ├── scripts.R └── slide.css ├── data ├── Clustering_Methods_Comparison.png ├── Core.assembly_tables.png ├── EnrichR.png ├── GO.png ├── GO_ORA_results.png ├── GO_SHOX.png ├── GSEA.png ├── GTF_Example.png ├── GTF_Example.pptx ├── Gene_set_interaction.png ├── HC-agglomerative.png ├── HC-divisive.png ├── Image_preparation.pptx ├── KEGG.jpeg ├── KEGG_database_categories.png ├── Kmeans_3.gif ├── Kmeans_3_DS.gif ├── Linkages.png ├── MSigDB.jpg ├── MSigDB_database.png ├── MSigDB_files │ ├── c2.cp.kegg.v6.2.symbols.gmt.txt │ ├── c2.cp.v6.2.symbols.gmt.txt │ ├── c3.tft.v6.2.symbols.gmt.txt │ ├── c5.bp.v6.2.symbols.gmt.txt │ └── h.all.v6.2.symbols.gmt.txt ├── Mahalanobis.png ├── ORA.png ├── ORA_Paulo_2019.png ├── PPI.png ├── Pathview_example.png ├── Pathway.jpeg ├── Reactome_Browser.png ├── Tokyo_Metro.jpeg ├── Wikipahtways.svg ├── boxplot.png ├── common │ ├── filezilla.png │ ├── mobaxterm.png │ ├── r.png │ ├── rstudio.png │ ├── supr-login.png │ ├── supr-projects.png │ ├── supr-request.png │ ├── versioning.png │ └── xquartz.png ├── counts_filtered.csv ├── counts_tpm.csv ├── counts_vst.csv ├── deseq_dispersion.png ├── dge_results.csv ├── gene_counts.csv ├── gene_counts_normalised_deseq2.Rds ├── gene_counts_original.tsv ├── gene_counts_raw.csv ├── gene_tpm_counts.csv ├── kmeans.gif ├── kmeans_DS.gif ├── lfc_shrink.png ├── metadata_original.csv ├── metadata_raw.csv ├── mock_pvc.Rds ├── mouse_genes.txt ├── mouse_go.txt ├── mouse_transcripts.txt ├── normalization_methods_composition.png ├── normalization_methods_depth.png ├── normalization_methods_length.png └── pvc.Rds ├── env_MacOSX.yml ├── env_linuxOrMobaXTerm.yml ├── env_renderSite.yml ├── home_content.Rmd ├── home_info.Rmd ├── home_precourse.Rmd ├── home_schedule.Rmd ├── index.Rmd ├── lab_annotation.Rmd ├── lab_assembly.Rmd ├── lab_dge.Rmd ├── lab_download.Rmd ├── lab_eda.Rmd ├── lab_functional.Rmd ├── lab_geoquery.Rmd ├── lab_igv.Rmd ├── lab_kallisto.Rmd ├── lab_mapping.Rmd ├── lab_preprocessing.Rmd ├── lab_qc_aftermapping.Rmd ├── lab_qc_beforemapping.Rmd ├── lab_quantification.Rmd ├── lab_r.Rmd ├── lab_smallrna.Rmd ├── lab_uppmax_intro.Rmd ├── schedule.csv ├── slide_after_mapping_qc.pdf ├── slide_after_sequencing_qc.pdf ├── slide_clustering.rmd ├── slide_clustering_paulo.pdf ├── slide_dge.Rmd ├── slide_dge_advanced.pdf ├── slide_functional.rmd ├── 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