Author: Felix G.M. Ernst and Denis L.J. Lafontaine
Date: 2026-04-30

# RNAmodR.Data: example data for RNAmodR packages

Felix G.M. Ernst and Denis L.J. Lafontaine

#### 2026-04-30

#### Package

RNAmodR.Data 1.27.0

# 1 Available resources

`RNAmodR.Data` contains example data for the `RNAmodR` and related packages. The data is provided as gff3, fasta and bam files.

Four sets of data with multiple files are included

    ## No methods found in package 'rtracklayer' for request: 'trackName<-' when loading 'AnnotationHubData'

    ## Warning: replacing previous import 'utils::findMatches' by
    ## 'S4Vectors::findMatches' when loading 'ExperimentHubData'

    library(RNAmodR.Data)

    eh <- ExperimentHub()
    ExperimentHub::listResources(eh, "RNAmodR.Data")

    ##  [1] "RNAmodR.Data.example.fasta"     "RNAmodR.Data.example.gff3"
    ##  [3] "RNAmodR.Data.example.bam.1"     "RNAmodR.Data.example.bam.2"
    ##  [5] "RNAmodR.Data.example.bam.3"     "RNAmodR.Data.example.RMS.fasta"
    ##  [7] "RNAmodR.Data.example.RMS.gff3"  "RNAmodR.Data.example.RMS.1"
    ##  [9] "RNAmodR.Data.example.RMS.2"     "RNAmodR.Data.example.AAS.fasta"
    ## [11] "RNAmodR.Data.example.AAS.gff3"  "RNAmodR.Data.example.bud23.1"
    ## [13] "RNAmodR.Data.example.bud23.2"   "RNAmodR.Data.example.trm8.1"
    ## [15] "RNAmodR.Data.example.trm8.2"    "RNAmodR.Data.example.wt.1"
    ## [17] "RNAmodR.Data.example.wt.2"      "RNAmodR.Data.example.wt.3"
    ## [19] "RNAmodR.Data.example.man.fasta" "RNAmodR.Data.example.man.gff3"
    ## [21] "RNAmodR.Data.snoRNAdb"

These resources are grouped based on topic. Please have a look at the following man pages:

- `?RNAmodR.Data.example` for general example data used for different purposes
- `?RNAmodR.Data.RMS` for example data for RiboMethSeq
- `?RNAmodR.Data.AAS` for example data for AlkAnilineSeq
- `?RNAmodR.Data.man` for small data set for man page examples
- `?RNAmodR.Data.snoRNAdb` for snoRNAdb as csv file

# 2 snoRNAdb

`RNAmodR.Data.snoRNAdb` consists of a table containing the published data from the snoRNAdb (Lestrade and Weber 2006). The can be loaded as a GRanges object.

    library(GenomicRanges)

    table <- read.csv2(RNAmodR.Data.snoRNAdb(), stringsAsFactors = FALSE)

    ## see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation

    ## loading from cache

    head(table, n = 2)

    # keep only the current coordinates
    table <- table[,1:7]
    snoRNAdb <- GRanges(seqnames = table$hgnc_symbol,
                  ranges = IRanges(start = table$position, width = 1),strand = "+",
                  type = "RNAMOD",
                  mod = table$modification,
                  Parent = table$hgnc_symbol,
                  Activity = CharacterList(strsplit(table$guide,",")))
    # convert to current gene name
    snoRNAdb <- snoRNAdb[vapply(snoRNAdb$Activity != "unknown",all,logical(1)),]
    snoRNAdb <- split(snoRNAdb,snoRNAdb$Parent)
    head(snoRNAdb)

    ## GRangesList object of length 6:
    ## $RNA18SN5
    ## GRanges object with 69 ranges and 4 metadata columns:
    ##        seqnames    ranges strand |        type         mod      Parent
    ##           <Rle> <IRanges>  <Rle> | <character> <character> <character>
    ##    [1] RNA18SN5        27      + |      RNAMOD          Am    RNA18SN5
    ##    [2] RNA18SN5        34      + |      RNAMOD           Y    RNA18SN5
    ##    [3] RNA18SN5        36      + |      RNAMOD           Y    RNA18SN5
    ##    [4] RNA18SN5        93      + |      RNAMOD           Y    RNA18SN5
    ##    [5] RNA18SN5        99      + |      RNAMOD          Am    RNA18SN5
    ##    ...      ...       ...    ... .         ...         ...         ...
    ##   [65] RNA18SN5      1643      + |      RNAMOD           Y    RNA18SN5
    ##   [66] RNA18SN5      1678      + |      RNAMOD          Am    RNA18SN5
    ##   [67] RNA18SN5      1692      + |      RNAMOD           Y    RNA18SN5
    ##   [68] RNA18SN5      1703      + |      RNAMOD          Cm    RNA18SN5
    ##   [69] RNA18SN5      1804      + |      RNAMOD          Um    RNA18SN5
    ##                              Activity
    ##                       <CharacterList>
    ##    [1]                        SNORD27
    ##    [2]               SNORA50A,SNORA76
    ##    [3]                SNORA69,SNORA55
    ##    [4]                        SNORA75
    ##    [5]                        SNORD57
    ##    ...                            ...
    ##   [65]                        SNORA41
    ##   [66]                        SNORD82
    ##   [67] SNORD70A,SNORD70B,SNORD70C,...
    ##   [68]                        SNORD43
    ##   [69]                        SNORD20
    ##   -------
    ##   seqinfo: 9 sequences from an unspecified genome; no seqlengths
    ##
    ## ...
    ## <5 more elements>

# 3 Sessioninfo

    sessionInfo()

    ## R version 4.6.0 RC (2026-04-17 r89917)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_GB              LC_COLLATE=C
    ##  [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: America/New_York
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] RNAmodR.Data_1.27.0      ExperimentHubData_1.39.0 AnnotationHubData_1.43.0
    ##  [4] futile.logger_1.4.9      GenomicRanges_1.65.0     Seqinfo_1.3.0
    ##  [7] IRanges_2.47.0           S4Vectors_0.51.1         ExperimentHub_3.3.0
    ## [10] AnnotationHub_4.3.0      BiocFileCache_3.3.0      dbplyr_2.5.2
    ## [13] BiocGenerics_0.59.0      generics_0.1.4           BiocStyle_2.41.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] tidyselect_1.2.1            dplyr_1.2.1
    ##  [3] blob_1.3.0                  filelock_1.0.3
    ##  [5] Biostrings_2.81.0           bitops_1.0-9
    ##  [7] fastmap_1.2.0               RCurl_1.98-1.18
    ##  [9] GenomicAlignments_1.49.0    XML_3.99-0.23
    ## [11] digest_0.6.39               lifecycle_1.0.5
    ## [13] KEGGREST_1.53.0             RSQLite_2.4.6
    ## [15] magrittr_2.0.5              compiler_4.6.0
    ## [17] rlang_1.2.0                 sass_0.4.10
    ## [19] tools_4.6.0                 yaml_2.3.12
    ## [21] lambda.r_1.2.4              rtracklayer_1.73.0
    ## [23] knitr_1.51                  S4Arrays_1.13.0
    ## [25] bit_4.6.0                   curl_7.1.0
    ## [27] DelayedArray_0.39.0         abind_1.4-8
    ## [29] BiocParallel_1.47.0         withr_3.0.2
    ## [31] purrr_1.2.2                 grid_4.6.0
    ## [33] SummarizedExperiment_1.43.0 cli_3.6.6
    ## [35] rmarkdown_2.31              crayon_1.5.3
    ## [37] stringdist_0.9.17           otel_0.2.0
    ## [39] httr_1.4.8                  rjson_0.2.23
    ## [41] BiocBaseUtils_1.15.0        RUnit_0.4.33.1
    ## [43] DBI_1.3.0                   cachem_1.1.0
    ## [45] parallel_4.6.0              AnnotationDbi_1.75.0
    ## [47] formatR_1.14                BiocManager_1.30.27
    ## [49] XVector_0.53.0              restfulr_0.0.16
    ## [51] matrixStats_1.5.0           vctrs_0.7.3
    ## [53] Matrix_1.7-5                jsonlite_2.0.0
    ## [55] bookdown_0.46               bit64_4.8.0
    ## [57] RBGL_1.89.0                 GenomicFeatures_1.65.0
    ## [59] jquerylib_0.1.4             glue_1.8.1
    ## [61] codetools_0.2-20            GenomeInfoDb_1.49.0
    ## [63] BiocVersion_3.24.0          BiocCheck_1.49.0
    ## [65] UCSC.utils_1.9.0            BiocIO_1.23.3
    ## [67] tibble_3.3.1                pillar_1.11.1
    ## [69] rappdirs_0.3.4              htmltools_0.5.9
    ## [71] graph_1.91.0                R6_2.6.1
    ## [73] httr2_1.2.2                 AnnotationForge_1.55.0
    ## [75] evaluate_1.0.5              OrganismDbi_1.55.1
    ## [77] Biobase_2.73.1              lattice_0.22-9
    ## [79] futile.options_1.0.1        png_0.1-9
    ## [81] Rsamtools_2.29.0            cigarillo_1.3.0
    ## [83] memoise_2.0.1               bslib_0.10.0
    ## [85] SparseArray_1.13.0          xfun_0.57
    ## [87] biocViews_1.81.0            MatrixGenerics_1.25.0
    ## [89] pkgconfig_2.0.3

# References

Lestrade, Laurent, and Michel J. Weber. 2006. “snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.” Nucleic Acids Research 34 (January): D158–D162. https://doi.org/10.1093/nar/gkj002.