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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 234 187

  2. modules modules Public

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

    Nextflow 276 692

  3. rnaseq rnaseq Public

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

    Nextflow 878 699

  4. sarek sarek Public

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

    Nextflow 395 402

  5. chipseq chipseq Public

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

    Nextflow 188 145

  6. eager eager Public

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

    Nextflow 143 80

Repositories

Showing 10 of 137 repositories
  • methylarray Public

    Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.

    nf-core/methylarray’s past year of commit activity
    Nextflow 1 MIT 0 0 0 Updated Oct 5, 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 276 MIT 692 423 (1 issue needs help) 135 Updated Oct 5, 2024
  • configs Public

    Config files used to define parameters specific to compute environments at different Institutions

    nf-core/configs’s past year of commit activity
    Nextflow 85 MIT 265 11 12 Updated Oct 5, 2024
  • website Public

    Code and files for the main nf-core website.

    nf-core/website’s past year of commit activity
    Astro 66 MIT 189 87 37 Updated Oct 5, 2024
  • fastquorum Public

    Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

    nf-core/fastquorum’s past year of commit activity
    Nextflow 20 MIT 9 12 (1 issue needs help) 1 Updated Oct 5, 2024
  • smrnaseq Public

    A small-RNA sequencing analysis pipeline

    nf-core/smrnaseq’s past year of commit activity
    Nextflow 73 MIT 124 13 (1 issue needs help) 1 Updated Oct 5, 2024
  • setup-nextflow Public

    A GitHub action to install Nextflow

    nf-core/setup-nextflow’s past year of commit activity
    TypeScript 12 MIT 4 8 (1 issue needs help) 3 Updated Oct 5, 2024
  • ops Public
    nf-core/ops’s past year of commit activity
    Python 1 2 23 10 Updated Oct 5, 2024
  • nascent Public

    Nascent Transcription Processing Pipeline

    nf-core/nascent’s past year of commit activity
    Nextflow 18 MIT 10 36 5 Updated Oct 4, 2024
  • circrna Public

    circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

    nf-core/circrna’s past year of commit activity
    Nextflow 44 MIT 21 15 4 Updated Oct 4, 2024
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