rgenie is a package 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 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, and then cDNA is generated. 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.
Two types of analyses can be run with rgenie: a grep-based analysis, which uses pattern matching to identify HDR vs. wild-type (WT) reads, and an alignment-based analysis, which uses all Cas9-generated alleles, including deletions. The analysis is run for a given region, which must have multiple replicates for both cDNA and gDNA. These analyses take as input a data.frame defining the region, and a data.frame defining replicates.
The result of an rgenie analysis is a list object with multiple tables, which depend on whether a grep or deletion analyses was done. Plotting functions take as input the result of one of these main rgenie analyses.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.