EpiTxDb.Sc.sacCer3 0.99.5
EpiTxDb.Sc.sacCer3 contains post-transcriptional RNA modifications from RMBase
v2.0 (Xuan et al. 2017) and tRNAdb (Jühling et al. 2009) and
can be accessed through the functions EpiTxDb.Sc.sacCer3.tRNAdb() and
EpiTxDb.Sc.sacCer3.RMBase()
library(EpiTxDb.Sc.sacCer3)etdb <- EpiTxDb.Sc.sacCer3.tRNAdb()## loading from cacheetdb## EpiTxDb object:
## # Db type: EpiTxDb
## # Supporting package: EpiTxDb
## # Data source: tRNAdb
## # Organism: Saccharomyces cerevisiae
## # Genome: sacCer3
## # Coordinates: per Transcript
## # Nb of modifications: 2990
## # Db created by: EpiTxDb package from Bioconductor
## # Creation time: 2020-02-26 10:43:09 +0100 (Wed, 26 Feb 2020)
## # EpiTxDb version at creation time: 0.99.0
## # RSQLite version at creation time: 2.2.0
## # DBSCHEMAVERSION: 1.0Modification information can be accessed through the typical function for an
EpiTxDb object, for example modifications():
modifications(etdb)## GRanges object with 2990 ranges and 3 metadata columns:
## seqnames ranges strand | mod_id mod_type
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] tA(AGC)D_tRNA 9 + | 1 m1G
## [2] tA(AGC)F_tRNA 9 + | 2 m1G
## [3] tA(AGC)G_tRNA 9 + | 3 m1G
## [4] tA(AGC)H_tRNA 9 + | 4 m1G
## [5] tA(AGC)J_tRNA 9 + | 5 m1G
## ... ... ... ... . ... ...
## [2986] tY(GUA)Q_tRNA 29 + | 3860 m2G
## [2987] tY(GUA)Q_tRNA 30 + | 3861 Y
## [2988] tY(GUA)Q_tRNA 40 + | 3862 i6A
## [2989] tY(GUA)Q_tRNA 66 + | 3863 m5U
## [2990] tY(GUA)Q_tRNA 67 + | 3864 Y
## mod_name
## <character>
## [1] m1G_9_tA(AGC)D_tRNA
## [2] m1G_9_tA(AGC)F_tRNA
## [3] m1G_9_tA(AGC)G_tRNA
## [4] m1G_9_tA(AGC)H_tRNA
## [5] m1G_9_tA(AGC)J_tRNA
## ... ...
## [2986] m2G_29_tY(GUA)Q_tRNA
## [2987] Y_30_tY(GUA)Q_tRNA
## [2988] i6A_40_tY(GUA)Q_tRNA
## [2989] m5U_66_tY(GUA)Q_tRNA
## [2990] Y_67_tY(GUA)Q_tRNA
## -------
## seqinfo: 258 sequences from sacCer3 genome; no seqlengthsFor a more detailed overview and explanation of the functionality of the
EpiTxDb class, have a look at the EpiTxDb package.
sessionInfo()## R Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.23-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] EpiTxDb.Sc.sacCer3_0.99.5 EpiTxDb_1.23.0
## [3] Modstrings_1.27.0 Biostrings_2.79.2
## [5] Seqinfo_1.1.0 XVector_0.51.0
## [7] AnnotationDbi_1.73.0 IRanges_2.45.0
## [9] S4Vectors_0.49.0 Biobase_2.71.0
## [11] AnnotationHub_4.1.0 BiocFileCache_3.1.0
## [13] dbplyr_2.5.1 BiocGenerics_0.57.0
## [15] generics_0.1.4 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] DBI_1.2.3 bitops_1.0-9
## [3] httr2_1.2.2 tRNAdbImport_1.29.0
## [5] biomaRt_2.67.0 rlang_1.1.6
## [7] magrittr_2.0.4 otel_0.2.0
## [9] matrixStats_1.5.0 compiler_4.6.0
## [11] RSQLite_2.4.5 GenomicFeatures_1.63.1
## [13] png_0.1-8 vctrs_0.6.5
## [15] txdbmaker_1.7.3 stringr_1.6.0
## [17] pkgconfig_2.0.3 crayon_1.5.3
## [19] fastmap_1.2.0 Rsamtools_2.27.0
## [21] rmarkdown_2.30 UCSC.utils_1.7.1
## [23] purrr_1.2.0 bit_4.6.0
## [25] xfun_0.54 cachem_1.1.0
## [27] cigarillo_1.1.0 Structstrings_1.27.0
## [29] GenomeInfoDb_1.47.2 jsonlite_2.0.0
## [31] progress_1.2.3 blob_1.2.4
## [33] DelayedArray_0.37.0 BiocParallel_1.45.0
## [35] parallel_4.6.0 prettyunits_1.2.0
## [37] R6_2.6.1 bslib_0.9.0
## [39] stringi_1.8.7 RColorBrewer_1.1-3
## [41] rtracklayer_1.71.0 GenomicRanges_1.63.1
## [43] jquerylib_0.1.4 bookdown_0.46
## [45] SummarizedExperiment_1.41.0 knitr_1.50
## [47] Matrix_1.7-4 tidyselect_1.2.1
## [49] dichromat_2.0-0.1 abind_1.4-8
## [51] yaml_2.3.11 codetools_0.2-20
## [53] curl_7.0.0 tRNA_1.29.0
## [55] lattice_0.22-7 tibble_3.3.0
## [57] withr_3.0.2 KEGGREST_1.51.1
## [59] S7_0.2.1 evaluate_1.0.5
## [61] xml2_1.5.1 pillar_1.11.1
## [63] BiocManager_1.30.27 filelock_1.0.3
## [65] MatrixGenerics_1.23.0 rex_1.2.1
## [67] RCurl_1.98-1.17 BiocVersion_3.23.1
## [69] hms_1.1.4 ggplot2_4.0.1
## [71] scales_1.4.0 glue_1.8.0
## [73] tools_4.6.0 BiocIO_1.21.0
## [75] GenomicAlignments_1.47.0 XML_3.99-0.20
## [77] grid_4.6.0 restfulr_0.0.16
## [79] cli_3.6.5 rappdirs_0.3.3
## [81] S4Arrays_1.11.1 dplyr_1.1.4
## [83] gtable_0.3.6 sass_0.4.10
## [85] digest_0.6.39 SparseArray_1.11.8
## [87] rjson_0.2.23 farver_2.1.2
## [89] memoise_2.0.1 htmltools_0.5.9
## [91] lifecycle_1.0.4 httr_1.4.7
## [93] bit64_4.6.0-1Jühling, Frank, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz. 2009. “TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes.” Nucleic Acids Research 37: D159–D162. https://doi.org/10.1093/nar/gkn772.
Xuan, Jia-Jia, Wen-Ju Sun, Peng-Hui Lin, Ke-Ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, and Jian-Hua Yang. 2017. “RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.” Nucleic Acids Research 46 (D1): D327–D334. https://doi.org/10.1093/nar/gkx934.