Disha - Bioinformatics (Level 2) Pathway

Certificates Summer 2021 Certificates R Shiny Transcriptomics App 2021
, ,
1

Technical Skills:

  • Refreshed my knowledge of the Transcriptomics Pipeline/how to read and analyze a bioinformatics paper
  • Experimented with RShiny interactive plotting
  • Analyzed UX requirements of planned educational app and responded to survey

Tools Used:

  • RShiny/RStudio
  • GSuite/Google Calendar
  • Trello
  • STEM-Away Forums
  • Slack

Soft Skills:

  • Project Management
  • Leadership
  • Presentation Skills
  • Onboarding Assistance

Achievement Highlights:

  • Set up all of the required collaboration for my team and successfully addressed all issues
  • Lead team meetings along with co-leads
  • Simultaneously worked on technical skills along with project management duties - ramped up RShiny knowledge

Challenges:

  • Collaborating with people in a new environment (different from school)
  • Had to ramp up very quickly with new PM tools
2

Technical Skills:

  • Completed data input stage of the Transcriptomics Pipeline
  • Developed overall understanding of project in order to drive the people and task management of our deliverable
  • Participated in UX interview about the R Shiny App user interface
  • Gained expertise in building automations between different PM tools (e.g., Sheets, AirTable, etc.)

Tools Used:

  • RShiny/RStudio
  • Additional collaboration tools in Week 2:
    • AirTable
    • Spacetime
    • Typeform

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Graduated from managing own team to helping out across all teams for the R Shiny App development
  • Created an efficient PM solution by using automations to link required tools and my understanding of the overall project
  • Worked effectively with team co-leads (Ashlesha and Marc), as well as overall project co-leads (Sam, Kelly, and Nikita)

Challenges:

  • Multitasking to cover many different areas
  • Had to get familiar with AirTable features beyond the starting concept of records
    • Automations
    • Iframe embeddings
3

Technical Skills:

  • Completed Quality Control stage of the Transcriptomics Pipeline using arrayQualityMetrics
  • Experimented with different quality control functions
    • Saw how different data structures allow for the use of specific functions
  • Learned what each output plot from arrayQualityMetrics displays and how to analyze the results
    • Gave a presentation about the outputs with Huikun (Kelly) to our team
  • Normalized data (after QC) using rma

Tools Used:

  • RShiny/RStudio
  • GitHub and GitHub Pages
  • Continued use of collaboration tools

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Created sub-group structure for the R Shiny App project with Sam and Nikita
  • Helped teammates with technical queries
  • Integrated session 2 participants and leads into project structure
  • Used feedback form to improve the effectiveness of sub-groups
    • Meetings, task assignments, collaboration, etc.

Challenges:

  • Sub-groups were struggling with initially planned structure, needed change
4

Technical Skills:

  • Completed DEG identification/ visual representation stage of the Transcriptomics Pipeline using limma, pheatmap, and EnhancedVolcano
    • Made a heatmap that grouped by sample types (cancer vs. control) for better visualization
    • Made two topTables, one with all of the genes and one with the top 100 DEGs; compared the second with that of the paper
  • Played around with different data structures to see which types were compatible with each function
  • Learned how to make a GitHub page for next steps in sub-group D of RShiny app development

Tools Used:

  • RShiny/RStudio
  • GitHub and GitHub Pages
  • Continued use of collaboration tools

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Finalized group structure for the R Shiny App project (sub-groups A and B1) with Nikita
  • Helped teammates with technical queries
  • Developed group structure for sub-group D and assigned relevant tasks for this week
  • Compared my DEG results with those of the paper and found that the results mostly overlapped
    • The differences likely due to removing fewer samples during QC

Challenges:

  • Was experimenting with visualizations and used too large of a structure as an input for pheatmap(), which caused R to crash
    • Unfortunately, had to go through all of the steps over again
  • Struggled a bit with balancing all of my tasks since our work for the app has ramped up this week.
5

Technical Skills:

  • Completed Functional analysis stage of the Transcriptomics Pipeline using msigdb and clusterProfiler
    • Changed the gene symbols to ENTREZIDs and ENSEMBLs for plots
    • Made a GSEA plot, a barplot and dotplot for enrichKEGG, and a barplot and dotplot for enrichGO
  • Produced code for normalization in R Shiny app with choice of RMA, GCRMA, and MAS5 normalization methods

Tools Used:

  • RShiny/RStudio
  • GitHub and GitHub Pages
  • Continued use of collaboration tools

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Group A/B1 completed the loading in of data/QC/normalization portion of R Shiny app
  • Finalized ideas for content and structure of GitHub page and adjusted template accordingly with with Kelly
  • Produced question set for blog portion of GitHub page

Challenges:

  • clusterProfiler was initially not loading in because of an error with a package “GO.db” not being compatible with my R version
  • Wasn’t able to set up happy hours this week, will need to try again next week
6

Technical Skills:

  • Completed Functional Analysis using Web Tools stage of the Transcriptomics Pipeline using DAVID, StringDB, and GEPIA
    • Specifically looked at the clustering view for DAVID and the gene AGER in GEPIA
  • Explored to find what the results of the Web Tools signified
    • DAVID: found out what clusters meant and how “Enrichment Score” correlates to significance of a cluster
    • String DB*: Clicked on the proteins associated with the top 10 genes in my top table to read about their function and see what they look like
  • Learned how to insert images that don’t have urls into GitHub pages

Tools Used:

  • RShiny/RStudio
  • GitHub and GitHub Pages
  • Continued use of collaboration tools

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Found a way to make a logarithmic scale for adjusting the fold change cut-off in R Shiny
  • Managed to resolve errors with inserting logo for the GitHub page using the inspect button
  • Wrapped up level 1 portion of the internship with our team’s participants
  • Gave a presentation with Kelly about StringDB and GEPIA
  • Got Modupe and Hale started with interviewing participants for our GitHub page’s blog

Challenges:

  • Initially wasn’t sure what exactly DAVID’s results were indicating; had to explore quite a bit to figure out what each of its features mean
  • Struggled with making the fold change scale in R Shiny volcano plot
    • The scale is logarithmic, but sliderInput() only allows for linear scales; had to use shinyWidgets to manually enter possible fold change values
7

Technical Skills:

  • Developed code for Functional Analysis for R Shiny app
    • Took Maryam’s code for GSEA plot and implemented it in R Shiny
    • Took my code for EnrichGO and EnrichKEGG and made sliders for numbers of categories shown
  • Learned about how to make tables in html to better the structure of our GitHub page
    • Thanks Keegan from UX/UI for helping us with this!
  • Found functions for making a button to download plots in R Shiny so that users can view EnrichGO/KEGG, gsea, and pathview plots better

Tools Used:

  • RShiny/RStudio
  • GitHub and GitHub Pages
  • Continued use of collaboration tools

Soft Skills:

  • Collaboration with co-leads and team
  • Project Management
  • Leadership
  • Presentation Skills
  • Feedback Collection

Achievement Highlights:

  • Gave a presentation to Anya and Ali about our R Shiny app, sMAP (standard microarray analysis pathway)
  • Found ways to make functional analysis steps of our app interactive
  • Finalized the GitHub page’s blog’s content and formatting
  • Uploaded all my individual contributions to our GitHub repo

Challenges:

  • Continued issues with clusterProfiler made it difficult to test my code for functional analysis in the app; ended up having to ask Nikita to test my code
  • The code for loading in raw data wasn’t functioning on most people’s devices
    • There was an error where the app couldn’t find the CEL files
    • I found a solution using the setwd() function, but that wouldn’t work if the user already had a directory of the same name as the temporary directory