Tools

Our tools and pipelines are open-source and freely available on GitHub. Visit the COMBINE Lab page!

Our group actively develops and maintains cutting-edge software and computational pipelines to support the scientific community. Below is a curated selection of our most recent and actively supported tools designed for next-generation genomic analysis.

PoreMeth2

PoreMeth2 is an R package for the identification of Differentially Methylated Regions from Nanopore methylation data (inferred by methcallers such as Dorado or Guppy) of paired samples and for their functional interpretation.
See the GitHub page.

MAGIBU

A modular R framework for stable methylation analysis. MAGIBU projects heterogeneous data (Array/Nanopore) onto a pre-computed reference. Features dynamic mapping and quantitative classification based on nearest class representatives to resolve heterogeneity.
See the GitHub page.

DNA LLM Benchmark

Inference pipelines used to evaluate genomic language models on single-nucleotide variant (SNV) datasets. Each notebook computes embedding-space distances (cosine, Euclidean, Manhattan, Jensen-Shannon, Hellinger, cross-entropy) between the reference and alternative sequence of each variant.
See the GutHub page.

SnakeBITE

A user-friendly Shiny GUI developed in python for customize and launch modular genomics data analysis pipelines using Snakemake, from Nanopore Oxford Technologies data.
See the GitHub page.

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