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@novoalab

Novoa Lab

Epitranscriptomics and RNA Dynamics Laboratory @crg (Barcelona, Spain)

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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 10

  2. EpiNano EpiNano Public

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

    Python 112 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

Repositories

Showing 10 of 30 repositories
  • SeqTagger Public

    Super-fast and accurate demultiplexing of direct RNA-seq runs.

    novoalab/SeqTagger’s past year of commit activity
    Jupyter Notebook 3 1 0 0 Updated Nov 18, 2024
  • polyTailor Public

    Poly-A tail length estimation from Nano3P-seq libraries

    novoalab/polyTailor’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 11, 2024
  • epitranscriptomic_fingerprinting Public

    Scripts used Milenkovic et al. "Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures" (Mol Cell 2024)

    novoalab/epitranscriptomic_fingerprinting’s past year of commit activity
    R 0 0 0 0 Updated Nov 8, 2024
  • Nano-tRNAseq Public

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

    novoalab/Nano-tRNAseq’s past year of commit activity
    Python 14 GPL-3.0 5 1 0 Updated Sep 19, 2024
  • EpiNano Public

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

    novoalab/EpiNano’s past year of commit activity
    Python 112 GPL-2.0 31 3 1 Updated Jun 30, 2024
  • 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)

    novoalab/m6ABasecaller’s past year of commit activity
    Jupyter Notebook 15 GPL-3.0 1 2 0 Updated Jun 12, 2024
  • basecalling_models Public

    Benchmarked base calling models for nanopore sequencing providing super high accuracy and improved RNA modification detection

    novoalab/basecalling_models’s past year of commit activity
    R 5 MIT 0 0 0 Updated May 9, 2024
  • mpileup2stats Public

    From samtools mpileup to stats of coverage, ref_nuc, mismatches, deletions, insertions, RT-stops

    novoalab/mpileup2stats’s past year of commit activity
    Perl 0 MIT 0 0 0 Updated May 8, 2024
  • modPhred Public

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

    novoalab/modPhred’s past year of commit activity
    Python 16 MIT 1 2 0 Updated Apr 29, 2024
  • Nm_Nanopore_Drosophila Public

    Detection of Nm sites from Nanopore DRS data

    novoalab/Nm_Nanopore_Drosophila’s past year of commit activity
    R 1 0 0 0 Updated Mar 27, 2024
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