This repository stores frequently re-used scripts for ingesting, analyzing, and visualizing a wide array of bioinformatic data (mainly genomic based assay data, i.e. RNA-seq, ChIP-seq, also chromatin contact (3C)).
3C-methods/ - analysis scripts and other code for working with 3C-based assays (Hi-C, HiChIP, MicroC, etc.)
compbio/ - scripts for differential expression testing, super enhancer identification, and 3D hub formation.
ORCA/ - scripts for analysis of ORCA data and simulated ORCA traces. All code related to polymer simulations is here.
scripts/ - miscellaneous scripts for file conversion, data preprocessing, plotting/data visualization, etc.
Not all of my code/projects at Penn are housed here. They can be found at:
- https://github.com/faryabiLab/dockerize-workflows - Containerized and reproducible NGS processing pipelines.
- https://github.com/Nuwah12/Demo-RNAseq-Pipeline - Simple step-by-step RNA-seq processing pipeline made as a teaching tool for non-computational coleagues.
- 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).