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    12 repositories

    • nf-circrna

      Public
      circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
      Nextflow
      •
      MIT License
      •26•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • nf-scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •178•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • nf-sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •421•0•0•0•Updated Nov 9, 2024Nov 9, 2024

    • images_quantify_red_in_blue_signal

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • nf-chipseq

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      •
      MIT License
      •149•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • nf-rnavar

      Public
      gatk4 RNA variant calling pipeline
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Jun 27, 2024Jun 27, 2024

    • nf-fetchngs

      Public
      Pipeline to fetch metadata and raw FastQ files from public databases
      Nextflow
      •
      MIT License
      •75•0•0•0•Updated May 21, 2024May 21, 2024

    • nf-hic

      Public
      Analysis of Chromosome Conformation Capture data (Hi-C)
      Nextflow
      •
      MIT License
      •56•0•0•0•Updated May 9, 2024May 9, 2024

    • nf-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 May 9, 2024May 9, 2024

    • nf-atacseq

      Public
      ATAC-seq peak-calling and QC analysis pipeline
      Nextflow
      •
      MIT License
      •124•0•0•0•Updated May 9, 2024May 9, 2024

    • Filter-A2A-loops-for-active-genes

      Public
      Python
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • nf-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 Mar 22, 2024Mar 22, 2024