shenkers/cfdscore

R package that implements the bulged CFD score calculation described by Doench et al 2016

CFDscoRe

This is an implementation of the CFD score from Doench et al 2016. There is no reference implementation of the CFD score calculation, and the available implementations are either incomplete (focusing only on the mismatch penalties) or are known to contain a bug in the calculation of DNA-bulge containing alignments.

Installation

From R run:

devtools::install_github('shenkers/CFDscoRe')

To do this the R package devtools must be installed.

Usage

For a given guide/target-site alignment, e.g.:

 guide: CA-TGCCGTGTGTACCATGAC
          *    *          * *
target: CAGTGCCATGTGTACCATCAGNGG

The CFD score of the alignment can be calculated by calling:

CFDscoRe::cfd_score('CA-TGCCGTGTGTACCATGAC', 'CAGTGCCATGTGTACCATCAG', 'GG')

This package also provides a function to search for the optimal alignment of a guide to a candidate sequence:

CFDscoRe::optimal_alignment('CATGCCGTGTGTACCATGAC', 'CAGTGCCATGTGTACCATCAGGG')