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

Magnipore: Differential single nucleotide changes of ONT signals

Metagene Profiling Analysis and Visualization

Online version of tool is live

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

NanoSpeech: a custom modification-aware basecaller

Repository for the R package RNAModR

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.

handful of tools that might be needed before or after HAMR

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

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

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.

High-throughput Workflow for Processing and Analyzing RNA-Seq Data