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

Rshiny app projects

1. Notes on Rshiny development (Github link click here)
2. Non-invasive prenatal testing (NIPT) (link click here)
3. Visualization of patterns of X chromosome inactivation (link click here)
4. Visualization of availability of scRNAseq data (link click 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 click here)
  • Updated the GUI for one of the pages (Github link click 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 click here
2. Parse GTEx dataset
   • Github link click here