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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 242 191

  2. modules modules Public

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

    Nextflow 284 721

  3. rnaseq rnaseq Public

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

    Nextflow 920 708

  4. sarek sarek Public

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

    Nextflow 410 417

  5. chipseq chipseq Public

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

    Nextflow 195 150

  6. eager eager Public

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

    Nextflow 148 81

Repositories

Showing 10 of 145 repositories
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 18 MIT 10 37 5 Updated Nov 21, 2024
  • references Public
    nf-core/references’s past year of commit activity
    Nextflow 3 MIT 4 10 0 Updated Nov 21, 2024
  • tools Public

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

    nf-core/tools’s past year of commit activity
    Python 242 MIT 191 257 35 Updated Nov 21, 2024
  • raredisease Public

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

    nf-core/raredisease’s past year of commit activity
    Nextflow 90 MIT 34 32 1 Updated Nov 21, 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 64 MIT 37 59 (5 issues need help) 4 Updated Nov 21, 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 284 MIT 721 454 (1 issue needs help) 165 Updated Nov 21, 2024
  • test-datasets Public

    Test data to be used for automated testing with the nf-core pipelines

    nf-core/test-datasets’s past year of commit activity
    105 MIT 352 31 9 Updated Nov 21, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    MDX 69 MIT 196 90 34 Updated Nov 21, 2024
  • ampliseq Public

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    nf-core/ampliseq’s past year of commit activity
    Nextflow 188 MIT 117 24 2 Updated Nov 21, 2024
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring’s past year of commit activity
    Nextflow 13 MIT 8 6 1 Updated Nov 21, 2024
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