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    22 repositories

    • Panorama-seq

      Public
      Panoramaseq: A Scalable Workflow for Spatial Transcriptomics Analysis
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Feb 28, 2026Feb 28, 2026

    • tailgenes

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • PeakPrime

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

    • BarcodeCalling_benchmark

      Public
      A nextflow pipeline that allows to recall dna barcodes from fastq files.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • Probe-enrichment-platform

      Public
      The motifs of the different probes of interest are mapped against the fastq files with using the SeqKit v2.10.0 software. Subsequently, different motifs are cou…
      Python
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • TruncalFlow

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • totalexRNAseq

      Public
      Code accompanying the total extracellular RNA sequencing protocol paper
      HTML
      •
      Other
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • QSP_nextflow

      Public
      Nextflow pipeline for RNAseq analysis (adapted from Lexogen QuantSeqPool)
      Nextflow
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • FUSIONprimerXL

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Sep 9, 2025Sep 9, 2025

    • CIRCprimerXL

      Public
      Python
      •
      Other
      •0•4•0•0•Updated Aug 20, 2025Aug 20, 2025

    • exRNAQC

      Public
      code for the extracellular Quality Control (exRNAQC) study
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • circRNA_benchmarking

      Public
      HTML
      •1•7•0•0•Updated Aug 18, 2024Aug 18, 2024

    • CiLiQuant

      Public
      Tool to assess relative circular to linear fraction
      Python
      •
      MIT License
      •1•1•0•0•Updated Jul 12, 2024Jul 12, 2024

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •970•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •462•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •849•0•0•0•Updated Feb 8, 2024Feb 8, 2024

    • plasmaONT

      Public
      Nextflow pipeline for Oxford Nanopore Technologies plasma RNA sequencing
      HTML
      •0•0•0•0•Updated Oct 19, 2023Oct 19, 2023

    • CIRCprimerXL_ONT

      Public
      circ primer design for ONT
      Python
      •
      Other
      •0•0•0•0•Updated Jun 29, 2023Jun 29, 2023

    • coverageplot

      Public
      HTML
      •0•0•0•0•Updated Oct 19, 2021Oct 19, 2021

    • covidpooling

      Public
      R
      •0•0•0•0•Updated Jun 9, 2021Jun 9, 2021

    • RNAexome

      Public
      scripts to process RNA exome sequencing data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 15, 2021Jan 15, 2021

    • queensgambit

      Public
      A Queens Gambit color palette for R
      R
      •
      Other
      •149•1•0•0•Updated Nov 17, 2020Nov 17, 2020