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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 288 736

  3. rnaseq rnaseq Public

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

    Nextflow 955 716

  4. sarek sarek Public

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

    Nextflow 413 420

  5. chipseq chipseq Public

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

    Nextflow 204 149

  6. eager eager Public

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

    Nextflow 154 82

Repositories

Showing 10 of 150 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 90 41 Updated Jan 10, 2025
  • sammyseq Public

    Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

    nf-core/sammyseq’s past year of commit activity
    Nextflow 1 MIT 5 1 1 Updated Jan 10, 2025
  • mcmicro Public

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    nf-core/mcmicro’s past year of commit activity
    Nextflow 8 MIT 16 23 4 Updated Jan 9, 2025
  • stats Public
    nf-core/stats’s past year of commit activity
    HTML 0 0 13 10 Updated Jan 9, 2025
  • 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 15 26 (4 issues need help) 4 Updated Jan 9, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 48 8 Updated Jan 9, 2025
  • modules Public

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

    nf-core/modules’s past year of commit activity
    Nextflow 288 MIT 736 461 (1 issue needs help) 185 Updated Jan 9, 2025
  • funcscan Public

    (Meta-)genome screening for functional and natural product gene sequences

    nf-core/funcscan’s past year of commit activity
    Nextflow 77 MIT 22 16 3 Updated Jan 9, 2025
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 245 MIT 192 274 36 Updated Jan 9, 2025
  • references Public
    nf-core/references’s past year of commit activity
    Nextflow 11 MIT 4 14 0 Updated Jan 9, 2025
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