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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 288 737

  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
  • 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 45 MIT 15 25 (3 issues need help) 3 Updated Jan 11, 2025
  • 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 11, 2025
  • spatialvi Public

    Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

    nf-core/spatialvi’s past year of commit activity
    Nextflow 53 MIT 20 5 1 Updated Jan 11, 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 737 464 (1 issue needs help) 186 Updated Jan 11, 2025
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 14 MIT 6 8 6 Updated Jan 10, 2025
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 48 8 Updated Jan 10, 2025
  • scnanoseq Public

    Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

    nf-core/scnanoseq’s past year of commit activity
    Nextflow 22 MIT 6 1 1 Updated Jan 10, 2025
  • airrflow Public

    B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

    nf-core/airrflow’s past year of commit activity
    Nextflow 55 MIT 37 20 4 Updated Jan 10, 2025
  • atacseq Public

    ATAC-seq peak-calling and QC analysis pipeline

    nf-core/atacseq’s past year of commit activity
    Nextflow 195 MIT 123 34 3 Updated Jan 10, 2025
  • raredisease Public

    Call and score variants from WGS/WES of rare disease patients.

    nf-core/raredisease’s past year of commit activity
    Nextflow 93 MIT 37 33 3 Updated Jan 10, 2025
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