EpiTxDb.Mm.mm10 0.99.6
EpiTxDb.Mm.mm10 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.Mm.mm10.tRNAdb() and
EpiTxDb.Mm.mm10.RMBase()
library(EpiTxDb.Mm.mm10)etdb <- EpiTxDb.Mm.mm10.tRNAdb()## snapshotDate(): 2020-09-03## loading from cacheetdb## EpiTxDb object:
## # Db type: EpiTxDb
## # Supporting package: EpiTxDb
## # Data source: tRNAdb
## # Organism: Mus musculus
## # Genome: mm10
## # Coordinates: per Transcript
## # Checked against sequence: Yes
## # Nb of modifications: 1032
## # Db created by: EpiTxDb package from Bioconductor
## # Creation time: 2020-02-26 10:43:52 +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 1032 ranges and 3 metadata columns:
## seqnames ranges strand | mod_id mod_type
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] chr1.tRNA1004-GluCTC 10 + | 1 m2G
## [2] chr1.tRNA1007-GluCTC 10 + | 2 m2G
## [3] chr1.tRNA1010-GluCTC 10 + | 3 m2G
## [4] chr1.tRNA709-GluCTC 10 + | 4 m2G
## [5] chr10.tRNA90-GluCTC 10 + | 5 m2G
## ... ... ... ... . ... ...
## [1028] chr13.tRNA90-MetCAT 57 + | 1891 m1A
## [1029] chr13.tRNA959-MetCAT 57 + | 1892 m1A
## [1030] chr13.tRNA995-MetCAT 57 + | 1893 m1A
## [1031] chr15.tRNA876-MetCAT 57 + | 1894 m1A
## [1032] chr3.tRNA792-MetCAT 57 + | 1895 m1A
## mod_name
## <character>
## [1] m2G_10_chr1.tRNA1004..
## [2] m2G_10_chr1.tRNA1007..
## [3] m2G_10_chr1.tRNA1010..
## [4] m2G_10_chr1.tRNA709-..
## [5] m2G_10_chr10.tRNA90-..
## ... ...
## [1028] m1A_57_chr13.tRNA90-..
## [1029] m1A_57_chr13.tRNA959..
## [1030] m1A_57_chr13.tRNA995..
## [1031] m1A_57_chr15.tRNA876..
## [1032] m1A_57_chr3.tRNA792-..
## -------
## seqinfo: 93 sequences from mm10 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 version 4.0.0 alpha (2020-04-07 r78171)
## 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-4-0/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-0/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.Mm.mm10_0.99.6 EpiTxDb_1.1.0 Modstrings_1.5.1
## [4] Biostrings_2.57.2 XVector_0.29.3 AnnotationDbi_1.51.3
## [7] IRanges_2.23.10 S4Vectors_0.27.12 Biobase_2.49.0
## [10] AnnotationHub_2.21.5 BiocFileCache_1.13.1 dbplyr_1.4.4
## [13] BiocGenerics_0.35.4 BiocStyle_2.17.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.2 bit64_4.0.4
## [3] shiny_1.5.0 assertthat_0.2.1
## [5] interactiveDisplayBase_1.27.5 askpass_1.1
## [7] BiocManager_1.30.10 blob_1.2.1
## [9] GenomeInfoDbData_1.2.3 Rsamtools_2.5.3
## [11] yaml_2.2.1 progress_1.2.2
## [13] BiocVersion_3.12.0 pillar_1.4.6
## [15] RSQLite_2.2.0 lattice_0.20-41
## [17] glue_1.4.2 digest_0.6.25
## [19] Structstrings_1.5.2 GenomicRanges_1.41.6
## [21] promises_1.1.1 colorspace_1.4-1
## [23] tRNA_1.7.1 htmltools_0.5.0
## [25] httpuv_1.5.4 Matrix_1.2-18
## [27] XML_3.99-0.5 pkgconfig_2.0.3
## [29] biomaRt_2.45.2 bookdown_0.20
## [31] zlibbioc_1.35.0 purrr_0.3.4
## [33] xtable_1.8-4 scales_1.1.1
## [35] later_1.1.0.1 BiocParallel_1.23.2
## [37] tibble_3.0.3 openssl_1.4.2
## [39] ggplot2_3.3.2 generics_0.0.2
## [41] ellipsis_0.3.1 SummarizedExperiment_1.19.6
## [43] GenomicFeatures_1.41.2 magrittr_1.5
## [45] crayon_1.3.4 mime_0.9
## [47] memoise_1.1.0 evaluate_0.14
## [49] xml2_1.3.2 tools_4.0.0
## [51] prettyunits_1.1.1 hms_0.5.3
## [53] matrixStats_0.56.0 lifecycle_0.2.0
## [55] stringr_1.4.0 munsell_0.5.0
## [57] tRNAdbImport_1.7.1 DelayedArray_0.15.7
## [59] compiler_4.0.0 GenomeInfoDb_1.25.10
## [61] rlang_0.4.7 grid_4.0.0
## [63] RCurl_1.98-1.2 rappdirs_0.3.1
## [65] bitops_1.0-6 rmarkdown_2.3
## [67] gtable_0.3.0 DBI_1.1.0
## [69] curl_4.3 R6_2.4.1
## [71] GenomicAlignments_1.25.3 knitr_1.29
## [73] dplyr_1.0.2 rtracklayer_1.49.5
## [75] fastmap_1.0.1 bit_4.0.4
## [77] stringi_1.4.6 Rcpp_1.0.5
## [79] vctrs_0.3.3 tidyselect_1.1.0
## [81] xfun_0.16Jühling, 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.