RNA editing tools in R

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Documentation for package ‘raer’ version 1.4.0

• 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()