This repository houses code developed during my tenure at UPenn as a bioinformatician in the Faryabi Lab. The code found here deals with the ingestion, analysis, and visualization of Next-Generation Sequencing (NGS) data, as well as utility functions to do a wide array of tasks common to bioinformatics and data analysis in Python and R. There are also a wide array of scripts for bioinformaticians working in a UNIX environment.
CodeWorkbench/
├── 3C-methods/ # Hi-C, HiChIP, Micro-C analysis
├── compbio/ # DE testing, super enhancers, 3D hubs
├── imaging/ # Code for image analysis (currently FISH and ORCA)
├── scripts/ # General-purpose plotting and utility scripts
├── convert/ # File format converters for common bioinformatics filetypes
├── misc/ # Miscellaneous scripts and helpers
├── DepMap/ # Tools for Cancer Dependency Map data
- https://github.com/faryabiLab/dockerize-workflows - Containerized, version controlled, and reproducible Next Generation Sequencing (NGS - RNAseq, ChIPseq, ATACseq) processing pipelines.
- https://github.com/Nuwah12/Demo-RNAseq-Pipeline - Simple step-by-step RNA-seq processing pipeline written in Bash made as a teaching tool for non-computational colleagues.
- https://github.com/Nuwah12/FISH-Spot-Calling - A simplistic workflow for calling spots on smRNA FISH images.
- https://github.com/Nuwah12/GENOVA2 - A fork of the popular 3C data visualization R package GENOVA, with added options for applying normalization to contact matrices.
- https://github.com/Nuwah12/EBV_Project - Code related to a project surrounding the interaction of an MCL cell line's genome with the Epstein-Barr Virus episome (coming soon, currently under construction).
In addition, my personal website includes more information on my work and career.