The Repguide R package is a beta development version to facilitate the design of guideRNAs for CRISPR/dCas9 targeting of repetitive DNA sequences, such as those derived from transposable elements.
Functionality
The basic workflow consists of exploring and selecting target sites, computing the guideRNA universe, and finding the optimal combination of guides that maximizes target-specific coverage.
Features include:
- Multi-species support
- Flexible genome annotation
- Black- and whitelisting
- Multiple sequence alignment
- Promoter identification
- Consensus positional targeting
- Genome-wide mapping
- On and off-target scoring
- Combinatorial optimization (multiple guides)
- High-quality reports
More details on the usage of Repguide is available in the package vignette.
Installation
# Install BiocManager (in case you haven't already) if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") # Install Repguide remotes::install_github(repo = 'tanaylab/repguide')
Note: Repguide requires R version 3.5 or higher. The package was tested on linux and macbook machines, but is currently not compatible on Windows. A typical application will require at least 4 GB RAM, but heavier use cases (e.g. large guideRNA universe) may require 8 GB RAM or more. For improved speed performance, we recommend a multi-CPU/core workstation.