crispr-cas

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

Tutorials for the crisprVerse

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

A guideRNA design tool for the modern era.

This repository includes scripts for sequencing data analysis

Implementation of the paper "AcrTransAct: Pre-trained Protein Transformer Models for the Detection of Type I Anti-CRISPR Activities"

PyCCTyper: Accelerated detection and subtyping of CRISPR-Cas

A computational pipeline leveraging HMM-based probabilistic modeling to systematically identify, annotate, and map bacterial macromolecular secretion systems, conjugative transfer machineries, and CRISPR-Cas arrays across Bacteroidales proteomes.

A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.

Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.