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    18 repositories

    • clipseq

      Public
      The primary analysis pipeline for CLIP samples.
      Nextflow
      •
      MIT License
      •4•1•2•1•Updated Jan 14, 2025Jan 14, 2025

    • flowbio

      Public
      A python library for interacting with the Flow API
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 14, 2024Dec 14, 2024

    • flow-nf

      Public
      Reusable modules used in Flow
      Nextflow
      •
      MIT License
      •0•0•0•2•Updated Dec 1, 2024Dec 1, 2024

    • nfcore-wrappers

      Public
      Contains wrapper pipelines around nf-core modules
      Nextflow
      •0•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •176•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • chipseq

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      •
      MIT License
      •149•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •717•0•0•0•Updated Dec 1, 2024Dec 1, 2024

    • differential-analysis

      Public
      R
      •0•0•0•1•Updated Oct 6, 2024Oct 6, 2024

    • scflow

      Public
      Complete analysis workflow for single-cell/nuclei RNA-sequencing data.
      Nextflow
      •
      MIT License
      •15•0•0•0•Updated Nov 17, 2023Nov 17, 2023

    • nextflow.py

      Public
      Python wrapper around Nextflow.
      nextflowpipelines
      Python
      •
      GNU General Public License v3.0
      •8•57•0•1•Updated Nov 14, 2023Nov 14, 2023

    • fetchngs

      Public
      Pipeline to fetch metadata and raw FastQ files from public and private databases
      Nextflow
      •
      MIT License
      •75•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • tools

      Public
      Python package with helper tools for the nf-core community.
      Python
      •
      MIT License
      •192•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •49•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •127•0•0•0•Updated Dec 8, 2022Dec 8, 2022

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      224•0•0•0•Updated Oct 29, 2022Oct 29, 2022

    • flow-demultiplex

      Public
      The Demultiplex pipeline used in Flow, using Ultraplex.
      0•0•0•0•Updated Oct 8, 2022Oct 8, 2022

    • imaps-nf

      Public
      Nextflow
      •2•0•4•1•Updated Sep 26, 2022Sep 26, 2022

    • ultraplex

      Public
      Ultra-fast 5' and 3' demultiplexer
      Python
      •
      Other
      •12•0•0•0•Updated Aug 30, 2021Aug 30, 2021