Package: raer 1.11.1

Kent Riemondy

raer: RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Authors:Kent Riemondy [aut, cre], Kristen Wells-Wrasman [aut], Ryan Sheridan [ctb], Jay Hesselberth [ctb], RNA Bioscience Initiative [cph, fnd]

raer_1.11.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
raer/json (API)

# Install 'raer' in R:

install.packages('raer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rnabioco/raer/issues

Pkgdown/docs site:https://rnabioco.github.io

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library

On BioConductor:raer-1.11.0(bioc 3.24)raer-1.10.0(bioc 3.23)

multiplecomparison rnaseq singlecell sequencing coverage epitranscriptomics featureextraction annotation alignment bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq curl bzip2 xz-utils zlib

6.00 score 10 stars 7 scripts 372 downloads 23 exports 71 dependencies

Last updated from:21099f47b1. Checks:1 NOTE, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	401
linux-devel-arm64	WARNING	630
linux-devel-x86_64	WARNING	706
source / vignettes	OK	3084
linux-release-arm64	WARNING	628
linux-release-x86_64	WARNING	702
macos-release-arm64	WARNING	504
macos-release-x86_64	WARNING	1354
macos-oldrel-arm64	WARNING	571
macos-oldrel-x86_64	WARNING	842
windows-devel	WARNING	625
windows-release	WARNING	749
windows-oldrel	WARNING	654
wasm-release	FAIL	384

Exports:annot_from_gr annot_snps calc_AEI calc_confidence calc_edit_frequency calc_scAEI correct_strand filter_clustered_variants filter_multiallelic filter_splice_variants FilterParam find_de_sites find_mispriming_sites find_scde_sites get_overlapping_snps get_scAEI_sites get_splice_sites make_de_object mock_rse pileup_cells pileup_sites raer_example read_sparray

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML XVector yaml

Introducing the raer package

Rendered fromraer.Rmdusingknitr::rmarkdown

Last update: 2025-07-14
Started: 2022-05-02

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

Package: raer 1.11.1

raer: RNA editing tools in R

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