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EpiTxDb

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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) 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.