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@nf-core

nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
README.md

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  1. tools tools Public

    Python package with helper tools for the nf-core community.

    Python 220 185

  2. modules modules Public

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    Nextflow 263 660

  3. rnaseq rnaseq Public

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Nextflow 824 678

  4. sarek sarek Public

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    Nextflow 357 391

  5. chipseq chipseq Public

    ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 177 144

  6. eager eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Nextflow 131 79

Repositories

Showing 10 of 133 repositories
  • tools Public

    Python package with helper tools for the nf-core community.

    nf-core/tools’s past year of commit activity
    Python 220 MIT 185 242 33 Updated Jul 26, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 64 MIT 182 81 36 Updated Jul 26, 2024
  • differentialabundance Public

    Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

    nf-core/differentialabundance’s past year of commit activity
    Nextflow 49 MIT 29 37 1 Updated Jul 26, 2024
  • modules Public

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    nf-core/modules’s past year of commit activity
    Nextflow 263 MIT 660 401 (1 issue needs help) 119 Updated Jul 26, 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`).

    nf-core/crisprseq’s past year of commit activity
    Nextflow 23 MIT 25 26 5 Updated Jul 26, 2024
  • variantbenchmarking Public

    A nextflow variant benchmarking pipeline - premature

    nf-core/variantbenchmarking’s past year of commit activity
    Nextflow 6 MIT 6 11 1 Updated Jul 26, 2024
  • eager Public

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    nf-core/eager’s past year of commit activity
    Nextflow 131 MIT 79 43 (2 issues need help) 4 Updated Jul 26, 2024
  • demultiplex Public

    Demultiplexing pipeline for sequencing data

    nf-core/demultiplex’s past year of commit activity
    Nextflow 37 MIT 36 30 4 Updated Jul 26, 2024
  • taxprofiler Public

    Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

    nf-core/taxprofiler’s past year of commit activity
    Nextflow 105 MIT 32 38 (1 issue needs help) 4 Updated Jul 26, 2024
  • sarek Public

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    nf-core/sarek’s past year of commit activity
    Nextflow 357 MIT 391 233 (3 issues need help) 30 Updated Jul 26, 2024
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