MUFFIN: a suite of tools for the analysis of functional sequencing data - Archive ouverte HAL
Article Dans Une Revue NAR Genomics and Bioinformatics Année : 2024

MUFFIN: a suite of tools for the analysis of functional sequencing data

Résumé

The large diversity of functional genomic assays allows for the characterization of non-coding and coding events at the tissue level or at a single-cell resolution. However, this diversity also leads to protocol differences, widely varying sequencing depths, substantial disparities in sample sizes, and number of features. In this work, we have built a Python package, MUFFIN, which offers a wide variety of tools suitable for a broad range of genomic assays and brings many tools that were missing from the Python ecosystem. First, MUFFIN has specialized tools for the exploration of the non-coding regions of genomes, such as a function to identify consensus peaks in peak-called assays, as well as linking genomic regions to genes and performing Gene Set Enrichment Analyses. MUFFIN also possesses a robust and flexible count table processing pipeline, comprising normalization, count transformation, dimensionality reduction, Differential Expression, and clustering. Our tools were tested on three widely different scRNA-seq, ChIP-seq and ATAC-seq datasets. MUFFIN integrates with the popular Scanpy ecosystem and is available on Conda and at https://github.com/pdelangen/Muffin.
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hal-04642848 , version 1 (10-07-2024)

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Pierre De langen, Benoit Ballester. MUFFIN: a suite of tools for the analysis of functional sequencing data. NAR Genomics and Bioinformatics, 2024, 6 (2), pp.lqae051. ⟨10.1093/nargab/lqae051⟩. ⟨hal-04642848⟩
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