software & codebooks & experimental protocols
snpGuide
This software designs CRISPR protospacers to target single nucleotide polymorphisms with base editors (ABE / CBE). It is free to use. Input required is an rsID or a txt file with rsIDs on each line.
https://baglaenkolab.shinyapps.io/snpGuide/ | https://github.com/ybaglaenko/snpGuide
hlaGuide
This software designs CRISPR protospacers to target or preserve HLA alleles. Example: Ablate HLA-B27:05 while preserving HLA-B07:02. It includes plotting, efficiency calculations based on deep learning, and off-target predictions.
A functioning alpha version is available. We are working on getting it hosted online and a github repo in place. Contact us for immediate use if desired.
CRAFTseq
As part of a larger manuscript - we have deposited all analysis codebooks and the full experimental protocol for this work. This is a single cell analysis of genomic DNA amplicons, 3’ RNA sequencing, and ADT sequencing. https://github.com/immunogenomics/craft-seq