rgenie is an R package to analyze the sequencing output from a set of GenIE experimental replicates. It can be used with either ATAC or RNA GenIE experiments.
First install devtools, and then install rgenie using devtools:
install.packages("devtools")
devtools::install_github("jeremy37/rgenie")
(rgenie used to be available on CRAN but was removed for administrative reasons, and I haven't managed to update it yet.)
GenIE (genome-editing interrogation of enhancers) is an experimental method to evaluate the effects of individual SNPs on either gene transcription (when RNA is the readout) or on chromatin accessibility (when ATAC is the readout).
Briefly, CRISPR-Cas9 is targeted near a SNP of interest, and typically an oligonucleotide for homology-directed repair (HDR) will be included. With the editing done in a pool of cells, the single nucleotide change can be achieved in a fraction of cell chromosomes, and the remaining chromosomes will either be wild-type or will have deletions in the region. For an RNA readout, you then extract both RNA and DNA from the pool of cells, and do multiple replicates to amplify an amplicon from each of these (genomic DNA and cDNA). rgenie can help to visualize the experiment and compute statistics for the effects of different alleles on gene transcription. For an ATAC readout the workflow is similar, except that ATAC is done instead of RNA extraction, and there are some differences in the amplification protocol, as described in the papers cited below.
This plot shows the set of alleles measured in a set of gDNA and cDNA replicates.
The rgenie Introduction vignette shows how to download example data and run an analysis for RNA.
The rgenie in depth vignette provides more details on the parameters for some methods and how to interpret results.
The rgenie for ATAC vignette shows how to run an analysis for a GenIE-ATAC experiment.
rgenie for ATAC: Sarah E Cooper, Jeremy Schwartzentruber, Eve L Coomber, Andrew R Bassett, Identification of functional regulatory variants in open chromatin using GenIE-ATAC, in preparation.
rgenie: Sarah E Cooper, Jeremy Schwartzentruber, Erica Bello, Eve L Coomber, Andrew R Bassett, Screening for functional transcriptional and splicing regulatory variants with GenIE, Nucleic Acids Research, Volume 48, Issue 22, 16 December 2020.
Feel free to submit an issue on github, or contact me:
jeremy37 at gmail dot com