epitranscriptomics

Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing

🧪 Ultrafast bisulfite

🧪 Pipeline for detecting Ψ modification

Analyse RNA feature distributions.

Base-conversion Sequencing Aligner

🧪 Optimized protocol for m6A-SAC-seq

Metagene Profiling Analysis and Visualization

Magnipore: Differential single nucleotide changes of ONT signals

Robust tRNA modification discovery from Nanopore direct tRNA sequencing

High-throughput pipeline for modified mRNA annotation and long non-coding RNA annotation

Online version of tool is live

NanoSpeech: a custom modification-aware basecaller

Repository for the R package RNAModR

Predicting m6A RNA modifications from Nanopore direct RNA-seq with a site-level graph neural network ensemble, applied to the SG-NEx cell lines.

CatMOD is a CatBoost-based feature-concatenation model for RNA modification recognition from ONT DRS.

NanoListener: a small suite of Python scripts to create custom training datasets for modification-aware basecaller models.

EpiRNA-Scanner, a publicly deployed web framework that processes sequences from 41 bases to over 100,000 bases without manual preprocessing. The system introduces Epitranscriptomic Boundary Contrast Scoring (EBCS), producing single-nucleotide resolution predictions anchored to degenerate DRACH motifs.

Annotates modomics RNA sequences for easy viewing of RNA modifications and nucleotide positions.

Hierarchical Bayesian framework for RNA modification detection from nanopore direct RNA sequencing (CUDA-accelerated DTW + HMM)

Database For miRNA mRNA Target Interactions, a bioinformatics platform designed to store and analyze microRNA-mRNA target interaction data. It provides a seamless user experience to help researchers investigate gene regulation pathways, identify binding sites, and streamline genomics research.