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@nf-core

nf-core

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

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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 284 722

  3. rnaseq rnaseq Public

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

    Nextflow 923 709

  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
  • drugresponseeval Public

    Pipeline for testing drug response prediction models in a statistically and biologically sound way.

    nf-core/drugresponseeval’s past year of commit activity
    Nextflow 5 MIT 1 4 1 Updated Nov 25, 2024
  • dualrnaseq Public

    Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

    nf-core/dualrnaseq’s past year of commit activity
    Nextflow 18 MIT 30 15 8 Updated Nov 25, 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 (1 issue needs help) 3 Updated Nov 25, 2024
  • scrnaseq Public

    A single-cell RNAseq pipeline for 10X genomics data

    nf-core/scrnaseq’s past year of commit activity
    Nextflow 214 MIT 172 53 (1 issue needs help) 4 Updated Nov 25, 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 91 34 Updated Nov 25, 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 722 454 (1 issue needs help) 177 Updated Nov 24, 2024
  • phaseimpute Public

    A bioinformatics pipeline to phase and impute genetic data

    nf-core/phaseimpute’s past year of commit activity
    Nextflow 17 MIT 14 12 2 Updated Nov 24, 2024
  • nf-core/spatialxe’s past year of commit activity
    Nextflow 5 MIT 2 28 1 Updated Nov 24, 2024
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 18 MIT 10 37 5 Updated Nov 23, 2024
  • nanostring Public

    An analysis pipeline for Nanostring nCounter expression data.

    nf-core/nanostring’s past year of commit activity
    Nextflow 13 MIT 8 8 2 Updated Nov 22, 2024