Refreshing my skills in R, R studio and basics of GitHub
Reading and evauluating the Long et al., 2019 paper on lung cancer
Understanding how R shiny works and the key features of this web application
Tools:
R, R Studio
R shiny basics
STEM-Away platform
Soft Skills
Learning more about my team members and fellow leads
Collaboration with leads to present first team meeting
Time Management, with STEM-Away and my other commitments
Achievement highlights
Getting started with STEM-Away and Level 2 project, familiarising myself with new format and structure of my Dashboard and STEM-Away forum
Hosting first team meeting with my co-lead and PM lead, with icebreakers to introduce all team members and a presentation to get the team introduced to the project and journal club
Going back to using R and R Studio along with learning about R Shiny and its components and structure
Working in R Studio further in the transcriptomics pipeline and deliverables for Module 2
Going ore in depth into R Shiny, and successfully managing to make my first Shiny App, called BMI calculator, while learning more about R Shiny themes, adding text, images, sliding bars to input data, and getting an output.
Also refreshed my GitHub basic knowledge, watching Collin’s tutorials and help from the mentors and technical leads.
Tools:
R, R Studio
R shiny
STEM-Away platform
Trello
GitHub
Soft Skills
Collaboration with leads within my team to organise the team meeting for the week, and also collaborating with leads across other teams to successfully complete the week’s deliverables before presenting to team members
Producing my first R Shiny product, knowing to get help from the technical lead, and using additional resources available to me
This was followed by presenting and showcasing my application to rest of the Bioinformatics team on a technical training session.
Achievement highlights
Successfully completing the week’s deliverables before the team meeting, and helping other team leads to prepare the presentations for the meeting, even though I was not able to make it.
Studying R Shiny in more depth, and creating my first R Shiny app
Understanding the new proposed project workflow, and also collaborating with team members from the UX pathway to organise interviews for next week and fill in google surveys.
Module 3 deliverables: using all 4 of the quality control packages: simpleaffy, ArrayQualityMetrics, AffyQCReport and affyPLM, to run quality checks on the genomic data and identify potential outliers
Worked with @irock194 to produce plots of the data output of affyPLM, creating RLE and NUSE boxplots, heat maps and also understanding the meaning of the clusters and the scales
For principal component analysis (PCA), managed to generate plots of PC1 vs PC2 and also ellipses around two clusters of normal and cancer groups to also identify further outliers
Tools:
R, R Studio
Collaboration tools for communication
Soft Skills
Collaboration with team members and other leads
Time Management and prioritisation of tasks
Presentation skills
Leadership
Achievement Highlights
Collaborating with another team member to complete the week’s deliverables together, and also troubleshooting and reaching out to mentor when required
Presenting these deliverables alongside with introducing the team to next week’s deliverables and working on those as well
Working on Stemaway tasks along with other commitments, and producing deliverables in time
Module 4 deliverables: successfully managing to run Limma statistical analysis on the cleaned dataset and generate topTable of differentially expressed genes. Also generated a volcano plot with similar results to the initial research paper.
R Shiny: Worked with Sneha in group B2 to develop a layout for our section in the app, which includes the sections of Quality Control and Normalisation.
Tools:
R, R Studio
Collaboration tools for communication
Figma for R Shiny Layout designing
Soft Skills
Collaboration with team members and other leads
Time Management and prioritisation of tasks
Presentation skills
Leadership
Achievement Highlights
Keeping up with the modules and weekly deliverables, and going to Lead OH to help when required.
Introducing the team to next week’s deliverables along with other team leads
Working on R Shiny and using figma to design a layout for QC and normalisation section of app
Module 5 deliverables: Taking the top differentially expressed genes from last week’s deliverables and understanding their functional implications using many Bioconductor packages in R
Functional analysis included Gene Ontology in all three areas of Molecular Functions, Biological Processes and Cellular Components
Also worked on GSEA cnet plot, and dotplots for enrichKEGG
Soft Skills
Collaboration with team members and other leads
Collaboration with other pathways
Presentation skills
Leadership
Achievement Highlights:
Completed the week’s deliverables in time before presenting them to interns at the weekly team meetings
Worked to understand designing layout of the app further, using figma and presenting these to the UX team and getting their inputs
Module 6 deliverables: Functional analysis of top DGE genes using web-based tools including EnrichR, David, Metascape, GEPIA and StringDB
Explored GEPIA further to generate survival analysis plots for AGER and other top genes
Understood the many functional analysis plots generated by Metascape, how the genes are clustered together in their common functions
Soft Skills
Collaboration with team members and other leads
Collaboration with other pathways
Presentation skills
Leadership
Achievement Highlights:
Completed the week’s deliverables in time before presenting them to interns at the weekly team meetings
Worked alongside Marc and Sneha to use three of the functional deliverable tools in the web, Metascape, EnrichR and GEPIA and analysing the results from these
Wrapping up final team meeting for the capstone project and the transcriptomics pipeline