This repository contains codes that are/were written from my 1st to my 20th day of internship and short explanations of what I did during the internship at Gebze Technical University, supervised by Asst. Prof. Dr. Tunahan ÇAKIR from Bioengineering Department.
Analyses were perfomed in Python and R, depend on the necessities. The final products are in (.ipynb extension) jupyter notebook files because this allows me to explain the analyses clearer. All of the analyses can be found in the ~/src folder and the .html/.pdf files can be found in the ~/report folder.
- Distribution of Log Fold Change
- MS3 Proteins Gene Set Enrichment Analysis
- RNA-Seq Genes Gene Set Enrichment Analysis
- msigDB Canonical Pathway Analysis Proteomics and RNA-Seq Genes
- Heatmaps of Normalized Counts
- Comparison between Up Regulated Genes Alzheimer's and Parkinson's Disease
- Volcano Plot of RNA-Seq and MS3 Proteomics Data
- Distribution of Log Fold Changes of Huntington's Disease and Comparison to Parkinson's Disease
- Gene Set Enrichment Analysis of Huntington's Disease
- Distribution of Log Fold Changes of Alzheimer's Disease**
- DESeq2-like Analyzer in Python (unsuccessful)
Tools
Final reports are reports that were written at the end of each stage, the first stage was developing the program to retrieve data sets from GEO Database while the second stage is analyzing the RNA-Seq data of Parkinson's disease. Final reports are in the .docx (Microsoft Word 2007++) extension.
- Stage 1: Report
- Stage 2: Report
Daily logs contain summary of what I did each day during the internship, I usually update them every weekend since during weekdays I mostly focused on understanding new things and working on the projects.
- Day 0 - January 17, 2017
- Day 1 - January 18, 2017
- Day 2 - January 19, 2017
- Day 3 - January 20, 2017
- Day 4 - January 23, 2017
- Day 5 - January 24, 2017
see more...
These are the collections of data that are used for the project/analyses, majority of these data are gathered from all over the internet, mostly from big databases. The data are stored in the ~/data folder.
- mRNA-Seq expression and MS3 proteomics profiling of human post-mortem BA9 brain tissue for Parkinson's Disease and neurologically normal individuals
- mRNA-Seq Expression profiling of human post-mortem BA9 brain tissue for Huntington's Disease and neurologically normal individuals
**Disclaimer: All images are mine and created by me unless stated otherwise.