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