CRISPRseek - Design of guide RNAs in CRISPR genome-editing systems
The package encompasses functions to find potential guide RNAs for the CRISPR-based genome-editing systems including the Base Editors and the Prime Editors when supplied with target sequences as input. Users have the flexibility to filter resulting guide RNAs based on parameters such as the absence of restriction enzyme cut sites or the lack of paired guide RNAs. The package also facilitates genome-wide exploration for off-targets, offering features to score and rank off-targets, retrieve flanking sequences, and indicate whether the hits are located within exon regions. All detected guide RNAs are annotated with the cumulative scores of the top5 and topN off-targets together with the detailed information such as mismatch sites and restrictuion enzyme cut sites. The package also outputs INDELs and their frequencies for Cas9 targeted sites.
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immunooncologygeneregulationsequencematchingcrispr
6.67 score 2 dependents 52 scripts 624 downloadsGUIDEseq - 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.
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immunooncologygeneregulationsequencingworkflowstepcrispr
4.42 score 22 scripts 692 downloadsREDseq - 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.
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sequencingsequencematchingpreprocessing
3.53 score 17 scripts 590 downloads