# RNA editing tools in R

## Documentation for package ‘raer’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annot_from_gr | Annotate sites using GRanges object
annot_snps | Annotate known SNP positions
annot_snps.GRanges | Annotate known SNP positions
annot_snps.SummarizedExperiment | Annotate known SNP positions
calc_AEI | Calculate the Adenosine Editing Index (AEI)
calc_confidence | Calculate confidence score for observing editing
calc_edit_frequency | Adds editing frequencies
calc_scAEI | Calculate the Adenosine Editing Index (AEI) in single cells
correct_strand | Apply strand correction using gene annotations
FilterParam | Generate base counts using pileup
filter_clustered_variants | Filter out clustered sequence variants
filter_multiallelic | Filter out multi-allelic sites
filter_splice_variants | Filter out sites near splice sites
find_de_sites | Perform differential editing
find_mispriming_sites | Find regions with oligodT mispriming
find_scde_sites | Identify sites with differential editing between cells in single cell datasets
get_overlapping_snps | Retrieve SNPs overlapping intervals
get_scAEI_sites | Calculate the Adenosine Editing Index (AEI) in single cells
get_splice_sites | Extract regions surrounding splice sites
make_de_object | Make summarized experiment object for differential editing analysis
mock_rse | Generate a small RangedSummarizedExperiment object for tests and examples
pileup_cells | Generate base counts per cell
pileup_sites | Generate base counts using pileup
raer_example | Provide working directory for raer example files.
read_sparray | Read sparseMatrix produced by pileup_cells()