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1. nanoRMS nanoRMS Public

   Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* et al., Nature Biotech 2021)

   Jupyter Notebook 23 11

2. EpiNano EpiNano Public

   Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

   Python 113 31

3. Nano3P_Seq Nano3P_Seq Public

   Nanopore 3' end-capture sequencing (Begik et al., bioRxiv 2021)

   Python 12 3

4. modPhred modPhred Public

   modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

   Python 16 1

5. m6ABasecaller m6ABasecaller Public

   An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

   Jupyter Notebook 15 1

6. Nano-tRNAseq Nano-tRNAseq Public

   Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)

   Python 14 5