Difference between revisions of "User:Jsu"

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===Week 8: 7/16===
===Week 8: 7/16===
*Began working on poster
*Began writing report for REU
===Week 9: 7/23===
===Week 9: 7/23===
*Completed poster and submitted it
*Worked on report
===Week 10: 7/30===
===Week 10: 7/30===
*Presented poster on Monday
*Finished powerpoint presentation
*Presented powerpoint on Wednesday
*Finished writing report
*Normalized data for integration step

Revision as of 20:36, 2 August 2018

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
  • Began writing report for REU

Week 9: 7/23

  • Completed poster and submitted it
  • Worked on report

Week 10: 7/30

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