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    16 repositories

    • samurai

      Public
      A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).
      bioinformaticsnextflowbioinformatics-pipelinenextflow-pipeline
      Nextflow
      •
      MIT License
      •0•13•16•0•Updated Jul 22, 2025Jul 22, 2025

    • mgikit-multiqc

      Public
      MultiQC plugin to parse and integrate reports generated by mgikit demultiplexer
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.6k•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • nf-core-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •889•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • PureCN

      Public
      Copy number calling and variant classification using targeted short read sequencing
      R
      •
      Artistic License 2.0
      •33•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •465•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • scnapattern

      Public
      A workflow to calculate SCNA patterns as described in Pesenti et al.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • checkQC

      Public
      CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
      Python
      •
      GNU General Public License v3.0
      •17•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • SAMURAI_paper_scripts

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • samurai-test-data

      Public
      Public data files for SAMURAI tests
      MIT License
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • pyjanitor

      Public
      Clean APIs for data cleaning. Python implementation of R package Janitor
      Python
      •
      MIT License
      •173•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • LFV-benchmark

      Public
      A pipeline to generate and benchmark synthetic datasets as described in Sergi et al., 2024.
      bioinformaticsgenomicsnextflow
      Python
      •
      MIT License
      •0•1•1•0•Updated Jan 21, 2024Jan 21, 2024

    • webhook-to-matrix-hookshot

      Public
      Translate webhooks from Slack to matrix-hookshot
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 8, 2024Jan 8, 2024

    • nf-core-test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •429•0•0•0•Updated May 30, 2023May 30, 2023

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      231•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • CINSignatureDiscovery

      Public
      Discovering copy number signatures from TCGA and new cohorts.
      R
      •
      Other
      •2•0•0•0•Updated Jun 28, 2022Jun 28, 2022