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1. PSC_study PSC_study Public

   This repository provides a comprehensive report of the study Geography-independent mucosal microbiota alterations in primary sclerosing cholangitis persist after liver transplantation.

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2. 16S-rRNA-amplicon-workflow 16S-rRNA-amplicon-workflow Public

   Nextflow pipeline for end-to-end taxonomic profiling of paired-end 16S rRNA amplicon data (V3–V4), supporting multiple ASV inference methods and classifiers.

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3. CdiffScreen CdiffScreen Public

   A Nextflow pipeline for detection and quantification of Clostridioides difficile PaLoc / CdtLoc toxin genes and antimicrobial-resistance gene (ARG) profiling against the CARD database.

   Nextflow

4. Metagenomics_workflow Metagenomics_workflow Public

   A Nextflow pipeline for taxonomic profiling of shotgun metagenomic data.

   Nextflow

5. nf-Infogut-16S nf-Infogut-16S Public

   Benchmarking framework for evaluating bioinformatics tools used in processing microbiome NGS data, including multiple error profiles, workflows, and parameter settings. This project contributes to …

   Nextflow 1

6. RNAseq_workflow RNAseq_workflow Public

   Reproducible Nextflow pipeline for bulk RNA-seq preprocessing: QC, adapter trimming, rRNA depletion, STAR alignment, and Salmon quantification, with aggregated MultiQC reporting. Containerized with…

   Nextflow