RMBase v3.0 is an upgraded version of RMBase that mainly focuses on the mechanism and function of diverse RNA modifications. RMBase v3.0 is a comprehensive and convenient platform for efficient studying RNA modifications from large amounts of epitranscriptome high-throughput sequencing data. It provides multiple interfaces and web-based tools to integrate 73 types of RNA modification among 62 species, uncover the relationships between RNA modifications with a series of interacting factors, and reveal the distribution patterns, biochemical mechanisms, evolutionary conservation of RNA modifications and their biological roles in human diseases.

DirectRMDB is a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology, it is the first ONT-based database of quantitative RNA modification profiles. DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies.

Plant RNA Modification Database (PRMD), which was established primarily to facilitate RNA modification researches, containing 20 plant species and providing an intuitive interface to display the information. Besides, PRMD provided convenient visualization and functional analysis tools, such as RMlevelDiff, RMplantVar, RNAmodNet and Blast to perform different analyses, and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (IGV) to visually display the analysis and statistical results.

PseUI was developed by using support vector machine based on three different kinds of features including position specific nucleotide propensity, nucleotide composition, and Pseudo nucleotide composition. Now it is for three different species including H. sapiens, M. musculus and S. cerevisiae.

RMDisease, a database of genetic variants that can affect RNA modifications. By integrating the prediction results of 18 different RNA modification prediction tools and also 303,426 experimentally-validated RNA modification sites, RMDisease identified a total of 202,307 human SNPs that may affect (add or remove) sites of eight types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G and Nm). These include 4,289 disease-associated variants that may imply disease pathogenesis functioning at the epitranscriptome layer. These SNPs were further annotated with essential information such as post-transcriptional regulations (sites for miRNA binding, interaction with RNA-binding proteins and alternative splicing) revealing putative regulatory circuits. A convenient graphical user interface was constructed to support the query, exploration and download of the relevant information.

RNAModR provides functions to map lists of genomic loci of RNA modifications to a reference mRNA transcriptome, and perform exploratory functional analyses of sites across the transcriptome trough visualisation and statistical analysis of the distribution of sites across transcriptome sections (5'UTR, CDS, 3'UTR).

The package is designed for transcriptomic visualization of RNA-related genomic features represented with genome-based coordinates with respect to the landmarks of RNA transcripts.

RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome.

RNAmod is a very convenient web-based platform for the meta-analysis and functional annotation of modifications on mRNAs. RNAmod uses the commonly used BED format chromosomal location information of mRNA modifications as input, which can be generated with common peak-calling tools, such as MACS, Exomepeaks and MetaTeak, or can be easily converted from other text formats.

ICE followed by NGS identifies adenosine-to-inosine editing. In this method, RNA is treated with acrylonitrile, while control RNA is untreated. Control and treated RNAs are reverse-transcribed and PCR-amplified. Inosines in RNA fragments treated with acrylonitrile cannot be reverse-transcribed. Deep sequencing of the cDNA prepared from control and treated RNA provides high-resolution reads of inosines in RNA fragments.

Ψ-seq is a method to transcriptome-wide quantitative mapping of Ψ, which has been used to identify the vast majority of Ψ sites in rRNA, tRNA and snRNA and dozens of novel sites within snoRNAs and mRNAs.

Pseudo-Seq detects pseudouridylation sites in ncRNAs with single-nucleotide resolution using high-throughput sequencing. Pseudo-Seq is very similar to PSI-seq, in that both methods use CMC to modify pseudouridines selectively and halt reverse transcription. However, Pseudo-Seq circularizes cDNA strands before PCR amplification and purification, instead of using ARTseq.

PSI-Seq (Pseudouridine Site Identification Sequencing) identifies RNA sequences containing pseudouridine sites using high-throughput sequencing. PSI-Seq uses N-Cyclohexyl-N_-(2-morpholinoethyl)carbodiimide (CMC) to modify pseudouridines selectively, effectively halting reverse transcription. The cDNA libraries are prepared by the ARTseq method.

ChIPseeker is a Bioconductor package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods for estimate the significance of overlap among ChIP peak data sets.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

POSTAR is a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (~23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes.