Coding portfolio

Below describes my coding projects and links to my Github repository

Bioinformatics workflow/pipeline

1. Pipeline for identification of variants from whole exome/genome (Github link here)
2. Pipeline for processing bulkRNAseq (Github link here)
3. Pipeline for processing single-cell RNAseq (Github link here)
4. Pipeline for identification of tumor variants and neoepitope (Github link here)
5. Pipeline for running analyses on UKB-RAP (Github link here)
6. Pipeline for running FUMA Cell type on the command line (Github link here)

Rshiny app projects

1. Notes on Rshiny development (Github link here)
2. Non-invasive prenatal testing (NIPT) (link here)
3. Visualization of patterns of X chromosome inactivation (link here)
4. Visualization of availability of scRNAseq data (link here)

Webtool development

• As part of my work at the VU, I am maintaining and updating a webtool called FUMA. Here are some of the tasks I have contributed to:
  • Implemented a functionality to delete jobs by administrator (Github link here)
  • Updated the GUI for one of the pages (Github link here)

Other

1. Develop a tool called vcfhelper in Python to aid with processing variant-calling-format (VCF) files.
   • vcfhelper extracts any annotations of interest of the VCF file which can then be used to plot for visualization
   • Github link here
2. Parse GTEx dataset
   • Github link here