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Markdowns/09_Annotation_Slides.Rmd

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+---
+title: "Annotation of RNA-seq results"
+date: "October 2024"
+output:
+  ioslides_presentation:
+    css: css/stylesheet.css
+    logo: images/CRUK_Cambridge_Institute.png
+    smaller: yes
+    widescreen: yes
+  beamer_presentation: default
+  slidy_presentation: default
+---
+
+## Differential Gene Expression Analysis Workflow {#less_space_after_title}
+
+<div style="line-height: 50%;"><br></div>
+
+<img src="images/01s_workflow_3Day.svg" class="centerimg" style="width: 80%; margin-top: 60px;">
+
+## Sources of Annotation
+
+#### Bioconductor annotation packages
+
+* Relies on Bioconductor updates to get latest version
+
+* Different database types from different sources
+
+#### Biomart
+
+* Web-based tool to access annotations from Ensembl
+
+* Always up to date
+
+* BiomaRt R-package allows use from inside R
+
+#### Annotation Hub
+
+* Similar to Bioconductor packages
+
+* Huge range of database types and species
+
+* Also relies on maintainers updating verions
+
+#### Direct downloads
+
+* Latest version from websites eg. Gencode
+
+* Non-model species
+
+
+