CRISPRseek - Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output indels and their frequencies for Cas9 targeted sites.
Last updated 4 months ago
immunooncologygeneregulationsequencematchingcrispr
3.40 score 98 dependencies 2 dependentsGUIDEseq - GUIDE-seq and PEtag-seq analysis pipeline
The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.
Last updated 4 months ago
immunooncologygeneregulationsequencingworkflowstepcrispr
1.51 score 171 dependenciesREDseq - Analysis of high-throughput sequencing data processed by restriction enzyme digestion
The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
Last updated 4 months ago
sequencingsequencematchingpreprocessing
0.49 score 124 dependencies