Difference between revisions of "User:Jsu"
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===Week 1: 5/29=== | ===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=== | ===Week 2: 6/4=== | ||
| Line 13: | Line 14: | ||
===Week 3: 6/11=== | ===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=== | ===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=== | ===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=== | ===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 === | ===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=== | ===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=== | ===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=== | ===Week 10: 7/30=== | ||
| + | *Presented poster on Monday | ||
| + | *Finished powerpoint presentation | ||
| + | *Presented powerpoint on Wednesday | ||
| + | *Finished writing report | ||
| + | *Normalized data for integration step | ||
Latest revision as of 15:36, 3 August 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
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
