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Update README.md
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Omabekee authored Sep 15, 2024
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4. **Functional Enrichment Analysis**: Used ShinyGO (with default parameters and GO biological process database) to identify pathways enriched in the upregulated genes. The results obtained from ShinyGO were saved in a .csv file and used for visualisation (find file in *output* directory).

5. **Visualisation of Pathways**: Visualised the top 5 upregulated pathways using the results obtained from the enrichment analysis to generate a lollipop plot (scaled by the \-log10 of the p-value to indicate pathway significance) for better clarity and interpretation of the enriched pathways.
**R Function**: *ggplot()* is used to create various plots in R, such as scatter plots, bar plots and lollipop plots in R, with customizations for layers, scales and themes.

**R Function**: *ggplot()* is used to create various plots in R, such as scatter plots, bar plots and lollipop plots in R, with customizations for layers, scales and themes.

### Biological Significance of Top Upregulated Pathways
In summary, the top three pathways all point to the adaptive ability of tumour cells to ensure their survival and proliferation, leading to metastasis.

### Directory Structure

* **/code**: This directory contains all the R codes used for data analysis and visualisation, for each step in the workflow.
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