| 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() |