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README.md
# EpiTxDb <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/devel/EpiTxDb/EpiTxDb.png" height="200" align="right"> <!-- badges: start --> [![R-CMD-check](https://github.com/FelixErnst/EpiTxDb/workflows/R-CMD-check-bioc-devel/badge.svg)](https://github.com/FelixErnst/EpiTxDb/actions/) [![BioC Build](https://bioconductor.org/shields/build/devel/bioc/EpiTxDb.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/EpiTxDb/) [![codecov](https://codecov.io/gh/FelixErnst/EpiTxDb/branch/devel/graph/badge.svg)](https://codecov.io/gh/FelixErnst/EpiTxDb) [![BioC Years](https://bioconductor.org/shields/years-in-bioc/EpiTxDb.svg)](https://doi.org/doi:10.18129/B9.bioc.EpiTxDb) <!-- 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](https://doi.org/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](https://doi.org/10.1093/nar/gkv1036).