crispr-analysis

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

Synthego ICE - Inference of CRISPR Editing software

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Flexible analysis of high-content CRISPR screening

Robust and efficient analysis of single-cell perturbation studies

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

ProTiler method for the analysis and visualization of CRISPR screens with tiling-sgRNA design

A program used to find indels on target gene edited by CRISPR/Cas9

Identify and annotate mutations from genome editing assays.

Anaylsis for 3D CRISPR screens. Rust core with Python wrapping.

InDels analysis of CRISPR lines by NGS amplicon sequencing technology for a multicopy gene family.

Bioinformatics pipeline to analyze CRISPR synthetic lethal and synthetic viable screens

Fork of Azimuth (Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency), updated to work with Python 3.10+

Analysis of CRISPR-mediated edits in NGS amplicon sequences of multi-copy gene families.

[This is an archived repository, see the current version in Arc Institute GitHub]

Analysis codes for high-throughput short read sequencing data. Especially for RCP-PCR experiments on clonal CRISPR KO samples.

CRISPR-Cas9 Excision Therapy Suitability

A python-driven pooled CRISPR-screen analysis pipeline developed at the Phillips Lab (University of Pennsylvania) tailored to batch execution at a HPC environment.