The R package for GenIE analysis is designed to analyze the next-generation sequencing
output from a set of GenIE experimental replicates. GenIE (genome-editing interrogation of enhancers)
is an experimental method to evaluate the effects of individual single-nucleotide polymorphisms (SNPs)
on gene transcription. It is based on targeted CRISPR-Cas9 genome editing in cultured cells to
produce indels at a target locus, optionally with a homology-dependent recombination (HDR) construct
to create precisely defined genomic changes. Following this, both genomic DNA (gDNA) and RNA are
extracted from the same pool of cells, then complementary DNA (cDNA) is generated from the RNA. Both
gDNA and cDNA are amplified with locus-specific PCR primers, in multiple replicates, and libraries of
the experimental replicates are prepared for next-generation sequencing. The sequencing data from each
replicate for each region should be aligned to either the full reference genome or to a locus-specific
(amplicon) reference genome for analysis by 'rgenie'.

Analysis of GenIE Experiments

package-ubuntu-20.04-r-4.0.5#cran#rgenie-1.0.0

<p>A list with a single result object from GenIE grep analysis for the MUL1 example.
</p>

<p>A one-item list with a grep_analysis result object.
</p>

package-ubuntu-20.04-r-4.0.5#cran#rgenie-1.0.0#docs#mul1_grep_results

mul1_grep_results

Description

Usage

Format

rgenie

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