1 Available resources

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()
## snapshotDate(): 2020-03-31
## downloading 1 resources
## retrieving 1 resource
## loading from cache
etdb
## 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: 1.0

Modification 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 seqlengths

For a more detailed overview and explanation of the functionality of the EpiTxDb class, have a look at the EpiTxDb package.

2 Sessioninfo

sessionInfo()
## R Under development (unstable) (2020-04-01 r78128)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] EpiTxDb.Sc.sacCer3_0.99.3 EpiTxDb_0.99.5           
##  [3] Modstrings_1.3.12         Biostrings_2.55.7        
##  [5] XVector_0.27.2            AnnotationDbi_1.49.1     
##  [7] IRanges_2.21.8            S4Vectors_0.25.14        
##  [9] Biobase_2.47.3            AnnotationHub_2.19.9     
## [11] BiocFileCache_1.11.4      dbplyr_1.4.2             
## [13] BiocGenerics_0.33.3       BiocStyle_2.15.6         
## 
## loaded via a namespace (and not attached):
##  [1] matrixStats_0.56.0            bitops_1.0-6                 
##  [3] assertive.models_0.0-2        bit64_0.9-7                  
##  [5] progress_1.2.2                httr_1.4.1                   
##  [7] GenomeInfoDb_1.23.16          assertive.datetimes_0.0-2    
##  [9] tools_4.1.0                   R6_2.4.1                     
## [11] colorspace_1.4-1              DBI_1.1.0                    
## [13] assertive.data_0.0-3          assertive.reflection_0.0-4   
## [15] tidyselect_1.0.0              prettyunits_1.1.1            
## [17] bit_1.1-15.2                  curl_4.3                     
## [19] compiler_4.1.0                cli_2.0.2                    
## [21] assertive.properties_0.0-4    xml2_1.3.0                   
## [23] DelayedArray_0.13.8           rtracklayer_1.47.0           
## [25] assertive.files_0.0-2         bookdown_0.18                
## [27] scales_1.1.0                  tRNA_1.5.2                   
## [29] askpass_1.1                   rappdirs_0.3.1               
## [31] stringr_1.4.0                 digest_0.6.25                
## [33] Rsamtools_2.3.7               rmarkdown_2.1                
## [35] assertive.numbers_0.0-2       pkgconfig_2.0.3              
## [37] htmltools_0.4.0               fastmap_1.0.1                
## [39] rlang_0.4.5                   RSQLite_2.2.0                
## [41] assertive_0.3-5               shiny_1.4.0.2                
## [43] BiocParallel_1.21.2           dplyr_0.8.5                  
## [45] RCurl_1.98-1.1                magrittr_1.5                 
## [47] GenomeInfoDbData_1.2.2        Matrix_1.2-18                
## [49] munsell_0.5.0                 Rcpp_1.0.4                   
## [51] fansi_0.4.1                   lifecycle_0.2.0              
## [53] stringi_1.4.6                 assertive.base_0.0-7         
## [55] yaml_2.2.1                    SummarizedExperiment_1.17.5  
## [57] zlibbioc_1.33.1               grid_4.1.0                   
## [59] blob_1.2.1                    promises_1.1.0               
## [61] crayon_1.3.4                  lattice_0.20-41              
## [63] tRNAdbImport_1.5.6            assertive.code_0.0-3         
## [65] GenomicFeatures_1.39.7        hms_0.5.3                    
## [67] knitr_1.28                    pillar_1.4.3                 
## [69] GenomicRanges_1.39.3          assertive.sets_0.0-3         
## [71] codetools_0.2-16              biomaRt_2.43.4               
## [73] XML_3.99-0.3                  glue_1.3.2                   
## [75] BiocVersion_3.11.1            Structstrings_1.3.5          
## [77] evaluate_0.14                 BiocManager_1.30.10          
## [79] vctrs_0.2.4                   httpuv_1.5.2                 
## [81] gtable_0.3.0                  openssl_1.4.1                
## [83] purrr_0.3.3                   assertive.strings_0.0-3      
## [85] assertthat_0.2.1              ggplot2_3.3.0                
## [87] xfun_0.12                     mime_0.9                     
## [89] xtable_1.8-4                  assertive.types_0.0-3        
## [91] later_1.0.0                   assertive.data.uk_0.0-2      
## [93] tibble_3.0.0                  GenomicAlignments_1.23.2     
## [95] memoise_1.1.0                 assertive.matrices_0.0-2     
## [97] ellipsis_0.3.0                assertive.data.us_0.0-2      
## [99] interactiveDisplayBase_1.25.0

References

Jühling, 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.