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    122 repositories

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •737•0•0•0•Updated Feb 26, 2024Feb 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
      •717•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •177•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • epitopeprediction

      Public
      A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
      Nextflow
      •
      MIT License
      •23•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • tools

      Public
      Python package with helper tools for the nf-core community.
      Python
      •
      MIT License
      •192•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • datasync

      Public
      nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • riboseq

      Public
      Pipeline for the analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting) data.
      Nextflow
      •
      MIT License
      •8•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • website

      Public
      Code and files for the main nf-core website.
      Astro
      •
      MIT License
      •196•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •420•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • vscode-extensionpack

      Public
      A VSCode extension pack for nf-core developers.
      MIT License
      •7•0•0•0•Updated Feb 25, 2024Feb 25, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •281•0•0•0•Updated Feb 25, 2024Feb 25, 2024

    • mhcquant

      Public
      Identify and quantify MHC eluted peptides from mass spectrometry raw data
      Nextflow
      •
      MIT License
      •27•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •363•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • mag

      Public
      Assembly and binning of metagenomes
      Nextflow
      •
      MIT License
      •115•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • methylseq

      Public
      Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
      Nextflow
      •
      MIT License
      •146•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • variantbenchmarking

      Public
      A nextflow variant benchmarking pipeline - premature
      Nextflow
      •
      MIT License
      •8•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • pangenome

      Public
      Renders a collection of sequences into a pangenome graph.
      Nextflow
      •
      MIT License
      •17•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • AzureTRE

      Public
      An accelerator to help organizations build Trusted Research Environments on Azure.
      Python
      •
      MIT License
      •148•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • differentialabundance

      Public
      Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
      Nextflow
      •
      MIT License
      •41•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •127•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      •
      MIT License
      •123•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • rnasplice

      Public
      rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
      Nextflow
      •
      MIT License
      •29•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • eager

      Public
      A fully reproducible and state-of-the-art ancient DNA analysis pipeline
      Nextflow
      •
      MIT License
      •82•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • crisprseq

      Public
      A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
      Nextflow
      •
      MIT License
      •27•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • rangeland

      Public
      Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • circrna

      Public
      circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
      Nextflow
      •
      MIT License
      •26•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • rnafusion

      Public
      RNA-seq analysis pipeline for detection gene-fusions
      Nextflow
      •
      MIT License
      •99•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • phageannotator

      Public
      Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
      Nextflow
      •
      MIT License
      •8•0•0•0•Updated Feb 22, 2024Feb 22, 2024

    • callingcards

      Public
      A pipeline for processing calling cards data
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Feb 22, 2024Feb 22, 2024

    • nascent

      Public
      Nascent Transcription Processing Pipeline
      Nextflow
      •
      MIT License
      •11•0•0•0•Updated Feb 22, 2024Feb 22, 2024