Difference between revisions of "User:Jsu"
From REU@MU
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*Read some related papers | *Read some related papers | ||
*Began working on function to create a heatmap | *Began working on function to create a heatmap | ||
| + | *Met with Dr. Bozdag and the whole lab: projects' updates and progress | ||
===Week 8: 7/16=== | ===Week 8: 7/16=== | ||
Revision as of 18:44, 13 July 2018
Contents
Week 1: 5/29
- Attended lab orientation and library orientation
- Created wiki user page
- Researched and practiced different methods of clustering genes on RStudio to determine the best suited method
- Met with my PhD student mentor for the project, Ziynet, and Dr. Bozdag: discussed papers
Week 2: 6/4
- RStudio on desktop kept freezing so requested for an account on the server
- Read related papers to see what clustering methods other studies used while waiting for code to run
- Read proposal for project
- Read papers similar to the project's topic
- Explored and read about different R clustering packages
- Completed the three RCR training modules
Week 3: 6/11
- Read articles and webpages about clustering in R while waiting for clustering code to run
- Finished practicing clustering on RStudio
- Met with Ziynet and Dr. Bozdag: discussed possible papers to support the pipeline
- Read a paper related to the project's topic
- Met with Ziynet: I discussed the paper I read and she told me to practice coexpression and correlation in RStudio
- Began researching and practicing how to calculate coexpression of genes on RStudio
Week 4: 6/18
- Finished writing the practice code for determining coexpressed genes
- Met with Ziynet and Dr. Bozdag: discussed possible pipelines for the project
- Read two papers related to the project's topic
- Met with Ziynet: I discussed the two papers I read
- Began researching how to determine the correlation between two different genomic datatypes
- Began writing the practice code for determining correlation between mRNA and miRNA
Week 5: 6/25
- Made the mini presentation on Monday & Tuesday
- Wrote and practiced how to present the mini presentation
- Presented on Thursday
- Downloaded and tidied miRNA and transcription factor (TF) datasets of miRNA/TFs and their target genes
- Created functions for both datasets to input miRNA/TF and output their target gene, and vice versa
Week 6: 7/2
- Tidied the same miRNA and TF datasets again; had to convert gene IDs to gene names
- Continued working on the correlation practice code
- Read three papers related to determining coexpression of genes
- Tidied a different miRNA dataset
- Created a classification function that predicts cancer subtype based on gene expression dataset
Week 7: 7/9
- Finished working on correlation practice code
- Created a correlation function to compute correlation between 2 datasets
- Started working on correlation function to compute pairwise correlation in 1 dataset
- Started writing final report
- Read some related papers
- Began working on function to create a heatmap
- Met with Dr. Bozdag and the whole lab: projects' updates and progress
