Some scripts I used during my master's final project:
- GSEXXXX.r: this files' names refer to GEO's entries that are being processed. Each file belongs to one of this datasets.
- join_datasets.r: this is the file used to integrate and join information and data among differeten datasets. Furthermore, it obtains DEGs that will be nodes in our network.
- create_netwokr.r: uses previously created interactome and previously obtained DEGs to map these DEGs over the interactome and so obtain out disease network.
- node_analysis.r: analysis results of Cytoscape to prioritaze certain amount of nodes which we will study as drug targets.
- promiscuity.r: studies our drug's promiscuity among our disease network.
- network.cys: Cytoscape file that contains the created disease network.
- funtional_analysis: directory containing files related to funtional analysis performed with BiNGO.
- functions: directory containing R functions used during this project.
- interactome.rda: interactome used to create our disease network. Obtained from Luck, K., Kim, DK., Lambourne, L. et al. A reference map of the human binary protein interactome. Nature 580, 402–408 (2020). Link: http://www.interactome-atlas.org/