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    13 repositories

    • nf-core-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •719•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •415•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • 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•3•8•0•Updated Oct 22, 2024Oct 22, 2024

    • scnapattern

      Public
      A workflow to calculate SCNA patterns as described in Pesenti et al.
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • pyjanitor

      Public
      Clean APIs for data cleaning. Python implementation of R package Janitor
      Python
      •
      MIT License
      •170•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • SAMURAI_paper_scripts

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • LFV-benchmark

      Public
      A pipeline to generate and benchmark synthetic datasets as described in Sergi et al., 2024.
      bioinformaticsgenomicsnextflow
      Python
      •
      MIT License
      •0•0•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
      •353•0•0•0•Updated May 30, 2023May 30, 2023

    • PureCN

      Public
      Copy number calling and variant classification using targeted short read sequencing
      R
      •
      Artistic License 2.0
      •32•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      221•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.3k•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • CINSignatureDiscovery

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