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

• Developed and maintained FUMA using PHP/Laravel, JavaScript, Python, R, and docker contributing to both the web application and underlying bioinformatics pipelines.
• Added single-cell RNA-seq datasets from 36 studies to the FUMA cell type module and expanded gene-ranking metrics to improve identification of relevant cell types for each phenotype.
• Implemented FLAMES as a new FUMA module to identify potential effector genes within genomic risk loci, integrating the analysis pipeline with the FUMA web interface.
• Implemented QTL analysis by integrating multiple QTL resources to investigate potential functional mechanisms underlying GWAS associations.
• Expanded FUMA gene-mapping capabilities by adding different types of QTLs as functional annotations.
• Developed administrator functionality to delete jobs and improve management of computational jobs.
• Implemented detailed job logging and downloadable log files, allowing users to troubleshoot failed jobs and reducing the time required to investigate errors.
• Added automatic GRCh38-to-GRCh37 coordinate conversion, simplifying data submission for users working with different genome builds.
• Implemented a 10-job-per-user limit for each FUMA module, improving resource management and preventing users from submitting excessive numbers of concurrent jobs.
• Wrote and maintained extensive technical documentation on Read the Docs, covering FUMA modules, input requirements, workflows, and troubleshooting.

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