Science Score: 44.0%
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Low similarity (3.7%) to scientific vocabulary
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Repository
Bachelor Thesis
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README.md
Bachelor Thesis
Computational Analysis of viral-host protein interactions: focus on E7 & POU5F1.
Researched and implemented a Python pipeline for the analysis of in-house and publicly available genomics and proteomics data. Regulatory and protein interaction networks were constructed and visualized using Plotly and NetworkX packages to extract information about a protein complexes.
CytoNet.ipynb & CytoNet.py - Read the input PPI datafiles and returns an appropriate data structure. - Calculate an interaction score based on IntAct Database scoring method. - Extract the common interactors of the input datafiles. - Visualize the PPI networks using plotly and networkx.
ComplexFinder.ipynb & ComplexFinder.py - Read the PPI datafiles and return appropriate data structures. - Read the HGNC datafiles and return appropriate datastructures. - Compare data and visualize the results as bar charts using matplotlib.
ChIPNet.ipynb & ChIPNet.py - Read the PPI, ChIP-Atlas and TCGA input datafiles. - Return an appropriate data structure for each input file. - Compare data and return the predicted gene targets.
Owner
- Login: MariosEft97
- Kind: user
- Repositories: 3
- Profile: https://github.com/MariosEft97
Citation (CITATION.cff)
message: "If you use this software, please cite it as below."
authors:
- family-names: Eftychiou
given-names: Marios
orcid: https://orcid.org/0000-0002-5929-6956
title: "Computational Analysis of virus-host protein interactions: a case study of HPV16 E7 oncogene and human POU5F1 transcription factor"
version: 2.5.0
date-released: 01-06-2021
url: "https://github.com/MariosEft97/bachelor_thesis"