raerdata: datasets and databases for use with the raer package

Introduction

The raerdata package contains datasets and databases used to illustrate functionality to characterize RNA editing using the raer package. Included in the package are databases of known human and mouse RNA editing sites. Datasets have been preprocessed to generate smaller examples suitable for quick exploration of the data and demonstration of the raer package.

Installation

if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

# The following initializes usage of Bioc devel
BiocManager::install(version = "devel")

BiocManager::install("raerdata")
library(raerdata)

RNA editing Atlases

Atlases of known human and mouse A-to-I RNA editing sites formatted into GRanges objects are provided.

REDIportal

The REDIportal is a collection of RNA editing sites identified from multiple studies in multiple species (Picardi et al. (2017)). The human (hg38) and mouse (mm10) collections are provided in GRanges objects, in either coordinate only format, or with additional metadata.

rediportal_coords_hg38()
## GRanges object with 15638648 ranges and 0 metadata columns:
##              seqnames    ranges strand
##                 <Rle> <IRanges>  <Rle>
##          [1]     chr1     87158      -
##          [2]     chr1     87168      -
##          [3]     chr1     87171      -
##          [4]     chr1     87189      -
##          [5]     chr1     87218      -
##          ...      ...       ...    ...
##   [15638644]     chrY  56885715      +
##   [15638645]     chrY  56885716      +
##   [15638646]     chrY  56885728      +
##   [15638647]     chrY  56885841      +
##   [15638648]     chrY  56885850      +
##   -------
##   seqinfo: 44 sequences from hg38 genome; no seqlengths

CDS recoding sites

Human CDS recoding RNA editing sites identified by Gabay et al. (2022) were formatted into GRanges objects. These sites were also lifted over to the mouse genome (mm10).

cds_sites <- gabay_sites_hg38()
cds_sites[1:4, 1:4]
## GRanges object with 4 ranges and 4 metadata columns:
##       seqnames    ranges strand |    GeneName
##          <Rle> <IRanges>  <Rle> | <character>
##   [1]     chr1    999279      - |        HES4
##   [2]     chr1   1014084      + |       ISG15
##   [3]     chr1   1281229      + |      SCNN1D
##   [4]     chr1   1281248      + |      SCNN1D
##       RefseqAccession_1,ExonNum_1,NucleotideSubstitution_1,AminoAcidSubstitution_1;…;RefseqAccession_N,ExonNum_N,NucleotideSubstitution_N,AminoAcidSubstitution_N
##                                                                                                                                                       <character>
##   [1]                                                                                                                                      NM_001142467.1,exon3..
##   [2]                                                                                                                                      NM_005101.3,exon2,c...
##   [3]                                                                                                                                      NM_001130413.3,exon2..
##   [4]                                                                                                                                      NM_001130413.3,exon2..
##          Syn/NonSyn Diversifying/Restorative/Syn
##         <character>                  <character>
##   [1] nonsynonymous                           NA
##   [2] nonsynonymous                           NA
##   [3]    synonymous                           NA
##   [4] nonsynonymous                           NA
##   -------
##   seqinfo: 23 sequences from hg38 genome; no seqlengths

Datasets

Whole genome and RNA sequencing data from NA12878 cell line

WGS and RNA-seq BAM and associated files generated from a subset of chromosome 4. Paths to files and related data objects are returned in a list.

NA12878()
## $bams
## BamFileList of length 2
## names(2): NA12878_RNASEQ NA12878_WGS
## 
## $fasta
## [1] "/github/home/.cache/R/ExperimentHub/131d4948b133_8469"
## 
## $snps
## GRanges object with 380175 ranges and 2 metadata columns:
##            seqnames    ranges strand |         name     score
##               <Rle> <IRanges>  <Rle> |  <character> <numeric>
##        [1]     chr4     10001      * | rs1581341342         0
##        [2]     chr4     10002      * | rs1581341346         0
##        [3]     chr4     10004      * | rs1581341351         0
##        [4]     chr4     10005      * | rs1581341354         0
##        [5]     chr4     10006      * | rs1209159313         0
##        ...      ...       ...    ... .          ...       ...
##   [380171]     chr4    999987      * | rs1577536513         0
##   [380172]     chr4    999989      * |  rs948695434         0
##   [380173]     chr4    999991      * | rs1044698628         0
##   [380174]     chr4    999996      * | rs1361920394         0
##   [380175]     chr4    999997      * |   rs59206677         0
##   -------
##   seqinfo: 1 sequence from hg38 genome; no seqlengths

GSE99249: RNA-Seq of Interferon beta treatment of ADAR1KO cell line

RNA-seq BAM files from ADAR1KO and Wild-Type HEK293 cells and associated reference files from chromosome 18 (Chung et al. (2018)).

GSE99249()
## $bams
## BamFileList of length 6
## names(6): SRR5564260 SRR5564261 SRR5564269 SRR5564270 SRR5564271 SRR5564277
## 
## $fasta
## [1] "/github/home/.cache/R/ExperimentHub/131d32ff4669_8310"
## 
## $sites
## GRanges object with 15638648 ranges and 0 metadata columns:
##              seqnames    ranges strand
##                 <Rle> <IRanges>  <Rle>
##          [1]     chr1     87158      -
##          [2]     chr1     87168      -
##          [3]     chr1     87171      -
##          [4]     chr1     87189      -
##          [5]     chr1     87218      -
##          ...      ...       ...    ...
##   [15638644]     chrY  56885715      +
##   [15638645]     chrY  56885716      +
##   [15638646]     chrY  56885728      +
##   [15638647]     chrY  56885841      +
##   [15638648]     chrY  56885850      +
##   -------
##   seqinfo: 44 sequences from hg38 genome; no seqlengths

10x Genomics 10k PBMC scRNA-seq

10x Genomics BAM file and RNA editing sites from chromosome 16 of human PBMC scRNA-seq library. Also included is a SingleCellExperiment object containing gene expression values, cluster annotations, cell-type annotations, and a UMAP projection.

pbmc_10x()
## $bam
## class: BamFile 
## path: /github/home/.cache/R/ExperimentHub/131d4689fda8_8311
## index: /github/home/.cache/R/ExperimentHub/131de3860cf_8312
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA 
## 
## $sites
## GRanges object with 15638648 ranges and 0 metadata columns:
##              seqnames    ranges strand
##                 <Rle> <IRanges>  <Rle>
##          [1]     chr1     87158      -
##          [2]     chr1     87168      -
##          [3]     chr1     87171      -
##          [4]     chr1     87189      -
##          [5]     chr1     87218      -
##          ...      ...       ...    ...
##   [15638644]     chrY  56885715      +
##   [15638645]     chrY  56885716      +
##   [15638646]     chrY  56885728      +
##   [15638647]     chrY  56885841      +
##   [15638648]     chrY  56885850      +
##   -------
##   seqinfo: 44 sequences from hg38 genome; no seqlengths
## 
## $sce
## class: SingleCellExperiment 
## dim: 36601 500 
## metadata(2): Samples mkrs
## assays(2): counts logcounts
## rownames(36601): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2
## rowData names(3): ID Symbol Type
## colnames(500): TGTTTGTCAGTTAGGG-1 ATCTCTACAAGCTACT-1 ...
##   GGGCGTTTCAGGACGA-1 CTATAGGAGATTGTGA-1
## colData names(8): Sample Barcode ... r celltype
## reducedDimNames(2): PCA UMAP
## mainExpName: NULL
## altExpNames(0):

ExperimentHub access

Alternatively individual files can be accessed from the ExperimentHub directly

library(ExperimentHub)
eh <- ExperimentHub()
raerdata_files <- query(eh, "raerdata")
data.frame(
    id = raerdata_files$ah_id,
    title = raerdata_files$title,
    description = raerdata_files$description
)
##        id                                                         title
## 1  EH8233                Rediportal RNA editing sites, all data, (mm10)
## 2  EH8234        Rediportal RNA editing sites, coordinates only, (mm10)
## 3  EH8235                Rediportal RNA editing sites, all data, (hg38)
## 4  EH8236        Rediportal RNA editing sites, coordinates only, (hg38)
## 5  EH8237                 Mouse adenosine-to-inosine RNA recoding sites
## 6  EH8238                 Human adenosine-to-inosine RNA recoding sites
## 7  EH8239                                          SRR5564260_chr18.bam
## 8  EH8240                                      SRR5564260_chr18.bam.bai
## 9  EH8241                                          SRR5564261_chr18.bam
## 10 EH8242                                      SRR5564261_chr18.bam.bai
## 11 EH8243                                          SRR5564269_chr18.bam
## 12 EH8244                                      SRR5564269_chr18.bam.bai
## 13 EH8245                                          SRR5564270_chr18.bam
## 14 EH8246                                      SRR5564270_chr18.bam.bai
## 15 EH8247                                          SRR5564271_chr18.bam
## 16 EH8248                                      SRR5564271_chr18.bam.bai
## 17 EH8249                                          SRR5564277_chr18.bam
## 18 EH8250                                      SRR5564277_chr18.bam.bai
## 19 EH8251                               Genome sequence of chr18 (hg38)
## 20 EH8252                                10k PBMC scRNA-seq library BAM
## 21 EH8253                          10k PBMC scRNA-seq library BAM index
## 22 EH8254               10k PBMC scRNA-seq library SingleCellExperiment
## 23 EH8255 Rediportal RNA editing sites, chr16, coordinates only, (hg38)
## 24 EH8405       WGS of NA12878 cell line, first megabase of chr4, (BAM)
## 25 EH8406       WGS of NA12878 cell line, first megabase of chr4, (BAI)
## 26 EH8407   RNA-seq of NA12878 cell line, first megabase of chr4, (BAM)
## 27 EH8408   RNA-seq of NA12878 cell line, first megabase of chr4, (BAI)
## 28 EH8409                                    SNPs from chr4 in dbSNP155
## 29 EH8410              Genome sequence of first megabase of chr4 (hg38)
##                                                                                                                                                                                               description
## 1     GRanges object containing 107,094 mouse RNA editing sites, mm10, additional columns describe editing site characteristics, as described by REDIPORTAL http://srv00.recas.ba.infn.it/atlas/help.html
## 2                                                                                                                                               GRanges object containing 107,094 mouse RNA editing sites
## 3  GRanges object containing 15,638,648 human RNA editing sites, hg38, additional columns describe editing site characteristics, as described by REDIPORTAL http://srv00.recas.ba.infn.it/atlas/help.html
## 4                                                                                                                                      GRanges object containing 15,638,648 human RNA editing sites, hg38
## 5                                                                                                                              GRanges object containing 1,160 mouse CDS recoding RNA editing sites, mm10
## 6                                                                                                                              GRanges object containing 1,517 human CDS recoding RNA editing sites, hg38
## 7                                                                                                                                                     ADAR1KO Interferon beta biological replicate 2, BAM
## 8                                                                                                                                                     ADAR1KO Interferon beta biological replicate 2, BAI
## 9                                                                                                                                                     ADAR1KO Interferon beta biological replicate 3, BAM
## 10                                                                                                                                                    ADAR1KO Interferon beta biological replicate 3, BAI
## 11                                                                                                                                                    ADAR1KO Interferon beta biological replicate 1, BAM
## 12                                                                                                                                                    ADAR1KO Interferon beta biological replicate 1, BAI
## 13                                                                                                                                                   Wildtype Interferon beta biological replicate 2, BAM
## 14                                                                                                                                                   Wildtype Interferon beta biological replicate 2, BAI
## 15                                                                                                                                                   Wildtype Interferon beta biological replicate 3, BAM
## 16                                                                                                                                                   Wildtype Interferon beta biological replicate 3, BAI
## 17                                                                                                                                                   Wildtype Interferon beta biological replicate 1, BAM
## 18                                                                                                                                                   Wildtype Interferon beta biological replicate 1, BAI
## 19                                                                                                                                                                        Genome sequence of chr18 (hg38)
## 20                                                                                                                          BAM alignments on chr16 from 10x Genomics 3' scRNA-seq library from 10k PBMCs
## 21                                                                                                                 BAM index of alignments on chr16 from 10x Genomics 3' scRNA-seq library from 10k PBMCs
## 22                                                                                          Preprocessed SingleCellExperiment containing UMI counts from 10x Genomics 3' scRNA-seq library from 10k PBMCs
## 23                                                                                                                                     GRanges object containing human RNA editing sites from chr16, hg38
## 24                                                                                                            Whole genome sequencing of NA12878 cell line, alignments from first megabase of chr4, (BAM)
## 25                                                                                                            Whole genome sequencing of NA12878 cell line, alignments from first megabase of chr4, (BAI)
## 26                                                                                                                     RNA sequencing of NA12878 cell line, alignments from first megabase of chr4, (BAM)
## 27                                                                                                                     RNA sequencing of NA12878 cell line, alignments from first megabase of chr4, (BAI)
## 28                                                                                                                                                SNPs from dbSNP155 within first megabase of chr4 (hg38)
## 29                                                                                                                                                       Genome sequence of first megabase of chr4 (hg38)
Session info 
sessionInfo()
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] ExperimentHub_3.3.2         AnnotationHub_4.3.2        
##  [3] BiocFileCache_3.3.0         dbplyr_2.6.0               
##  [5] SingleCellExperiment_1.35.2 SummarizedExperiment_1.43.0
##  [7] Biobase_2.73.2              MatrixGenerics_1.25.0      
##  [9] matrixStats_1.5.0           Rsamtools_2.29.0           
## [11] Biostrings_2.81.9           XVector_0.53.0             
## [13] rtracklayer_1.73.0          GenomicRanges_1.65.4       
## [15] Seqinfo_1.3.2               IRanges_2.47.5             
## [17] S4Vectors_0.51.10           BiocGenerics_0.59.12       
## [19] generics_0.1.4              raerdata_1.11.0            
## [21] BiocStyle_2.41.0           
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.1         dplyr_1.2.1              blob_1.3.0              
##  [4] filelock_1.0.3           bitops_1.1-0             fastmap_1.2.0           
##  [7] RCurl_1.98-1.20          GenomicAlignments_1.49.2 XML_3.99-0.25           
## [10] digest_0.6.39            lifecycle_1.0.5          KEGGREST_1.53.6         
## [13] RSQLite_3.53.3           magrittr_2.0.5           compiler_4.6.1          
## [16] rlang_1.3.0              sass_0.4.10              tools_4.6.1             
## [19] yaml_2.3.12              knitr_1.52               S4Arrays_1.13.2         
## [22] bit_4.6.0                curl_8.0.0               DelayedArray_0.39.8     
## [25] abind_1.4-8              BiocParallel_1.47.0      withr_3.0.3             
## [28] purrr_1.2.2              sys_3.4.3                grid_4.6.1              
## [31] cli_3.6.6                rmarkdown_2.32           crayon_1.5.3            
## [34] otel_0.2.0               httr_1.4.9               rjson_0.2.23            
## [37] BiocBaseUtils_1.15.1     DBI_1.3.0                cachem_1.1.0            
## [40] parallel_4.6.1           AnnotationDbi_1.75.2     BiocManager_1.30.27     
## [43] restfulr_0.0.17          vctrs_0.7.3              Matrix_1.7-6            
## [46] jsonlite_2.0.0           bit64_4.8.6              maketools_1.3.2         
## [49] jquerylib_0.1.4          glue_1.8.1               codetools_0.2-20        
## [52] BiocVersion_3.24.0       BiocIO_1.23.3            tibble_3.3.1            
## [55] pillar_1.11.1            rappdirs_0.3.4           htmltools_0.5.9         
## [58] R6_2.6.1                 httr2_1.3.0              evaluate_1.0.5          
## [61] lattice_0.23-1           png_0.1-9                cigarillo_1.3.1         
## [64] memoise_2.0.1            bslib_0.12.0             SparseArray_1.13.4      
## [67] xfun_0.61                buildtools_1.0.0         pkgconfig_2.0.3
Chung, Hachung, Jorg J A Calis, Xianfang Wu, et al. 2018. “Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown.” Cell 172 (4): 811–824.e14. https://doi.org/10.1016/j.cell.2017.12.038.
Gabay, Orshay, Yoav Shoshan, Eli Kopel, et al. 2022. “Landscape of Adenosine-to-Inosine RNA Recoding Across Human Tissues.” Nat. Commun. 13 (1): 1184. https://doi.org/10.1038/s41467-022-28841-4.
Picardi, Ernesto, Anna Maria D’Erchia, Claudio Lo Giudice, and Graziano Pesole. 2017. “REDIportal: A Comprehensive Database of A-to-I RNA Editing Events in Humans.” Nucleic Acids Res. 45 (D1): D750–57. https://doi.org/10.1093/nar/gkw767.