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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 245 192

  2. modules modules Public

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

    Nextflow 287 736

  3. rnaseq rnaseq Public

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

    Nextflow 942 713

  4. sarek sarek Public

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

    Nextflow 413 417

  5. chipseq chipseq Public

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

    Nextflow 200 150

  6. eager eager Public

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

    Nextflow 153 82

Repositories

Showing 10 of 148 repositories
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 70 MIT 194 93 40 Updated Dec 24, 2024
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 12 MIT 5 8 6 Updated Dec 24, 2024
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 18 MIT 10 36 4 Updated Dec 23, 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 287 MIT 736 464 (1 issue needs help) 188 Updated Dec 23, 2024
  • rnafusion Public

    RNA-seq analysis pipeline for detection of gene-fusions

    nf-core/rnafusion’s past year of commit activity
    Nextflow 147 MIT 98 43 5 Updated Dec 23, 2024
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 48 9 Updated Dec 23, 2024
  • methylseq Public

    Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    nf-core/methylseq’s past year of commit activity
    Nextflow 150 MIT 145 22 (1 issue needs help) 4 Updated Dec 23, 2024
  • scdownstream Public

    A single cell transcriptomics pipeline for QC, integration and making the data presentable

    nf-core/scdownstream’s past year of commit activity
    Nextflow 44 MIT 13 25 (4 issues need help) 3 Updated Dec 23, 2024
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq’s past year of commit activity
    Nextflow 76 MIT 126 10 (1 issue needs help) 1 Updated Dec 23, 2024
  • chipseq Public

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

    nf-core/chipseq’s past year of commit activity
    Nextflow 200 MIT 150 16 (1 issue needs help) 5 Updated Dec 23, 2024
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