This repo contains code contributions from Elianna Kondylis and Jacklyn Luu during the summer/fall of 2021.
- Establish pipeline to process raw sequencing data from CRISPR screen experiments
- Create data visualizations to compare CRISPR screen data across different papers and families of viruses
- Incorporate datavizs into Infected Cell portal
- infected-cell-dash-compare (directory): dash app to compare 2 CRISPR screen experiments
- infected-cell-dash_template (directory): template for dash app
- infected-cell-portal (directory): Reach app with prototype CRISPR screen portal
- notebooks_elikond: work from Elianna Kondylis
- notebooks_jl: work from Jacklyn Luu
- Workflows: directory with makefile that takes fastq data (treatment and control) and Fred Hutch's Nextflow pipeline to create count tables and run RRA and RRAflute