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# EpiTxDb <img src="" height="200" align="right"> <!-- badges: start --> [![R-CMD-check](]( [![BioC Build](]( [![codecov](]( [![BioC Years](]( <!-- badges: end --> The epitranscriptome includes all post-transcriptional modifications of the RNA and describes and additional layer of information encoded on RNA. Like the term epigenome it is not about a change in nucleotide sequences, but the addition of functional elements through modifications. With the development of high throughput detection strategies for specific RNA modifications, such as miCLIP and Pseudo-Seq amongst other, a large number of modified positions have been identified and were summarized via the RMBase project ([Xuan et al. 2017, Sun et al. 2015](#Literature)) project. To make these information avaialble within the Bioconductor universe `EpiTxDb` was developed, which facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with. # Installation The current version of the `EpiTxDb` package is available from Bioconductor. ## Github ``` remotes::install_github("FelixErnst/EpiTxDb") # library(EpiTxDb) ``` ## Bioconductor ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("EpiTxDb") library(EpiTxDb) ``` # Literature - Jia-Jia Xuan, Wen-Ju Sun, Ke-Ren Zhou, Shun Liu, Peng-Hui Lin, Ling-Ling Zheng, Liang-Hu Qu, Jian-Hua Yang (2017): "RMBase v2.0: Deciphering the Map of RNA Modifications from Epitranscriptome Sequencing Data." Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D327–D334. doi:[10.1093/nar/gkx934]( - Wen-Ju Sun, Jun-Hao Li, Shun Liu, Jie Wu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang (2018): "RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data", Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D259–D265. doi:[10.1093/nar/gkv1036](