User:Jsu

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

Week 8: 7/16

• Began working on poster
• Continued writing report
• Downloaded and began tidying 2 more TF datasets
• Completed pairwise correlation function

Week 9: 7/23

• Completed poster and submitted it
• Worked on report
• Finished tidying the TF datasets
• Read some related papers

Week 10: 7/30

• Presented poster on Monday
• Finished powerpoint presentation
• Presented powerpoint on Wednesday
• Finished writing report
• Normalized data for integration step