Pubudu Nawarathna

A highly responsible, self motivated, progress focused punctual team player graduated from McGill University and with more than 3 years of working experience in Bioinformatics Pipeline development, NGS data analysis and hands-on experience with linux based HPCs.

My Portfolio

1. Bioinformatics Pipeline Development (Python and Bash)

Few of my individual contributions to development of pipelines /protocols for the GenPipes workflow Management System.

• Development of epiQC pipeline to assess the quality of ChIP-Seq signal tracks.
  • epiQC
  • chromImpute
• Technical Documentation for epiQC
• Addition of DiffBind R package to perform differential binding analysis to the ChiP-Seq pipeline.
  • R script to run the analysis
    • The script generates an automated HTML report using R Markdown render function.
  • The script which internally calls the DiffBind.R in order to run the analysis is here.
  • A sample output HTML report is here.
• A Nextflowpipeline for genome scaffolding using Hi-C Seq reads is here.

2. Links to two of my shiny Apps.

• Pathway Enrichment Analysis web application.
  • The app is hosted here
  • https://github.com/pubudumanoj/pathway_analysis
• Creating ID card for fule pass (A Country Specific App).
  • https://github.com/pubudumanoj/fuel_pass
  • The app is hosted here.

3. YouTube Demo Videos I created.

• Introduction to GenPipes.
• How to run Genpipes in Docker.

4. LinkedIn Learning Certificates

• AWS Essential Training
• Data Wrangling in R
• Artificial Intelligence Foundations: Machine Learning
• Artificial Intelligence Foundations: Thinking Machines
• Machine Learning with Python: Foundations

5. Hacker Rank Certificates

• R