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@nf-core

nf-core

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

Pinned

  1. tools tools Public

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

    Python 216 178

  2. modules modules Public

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

    Nextflow 256 644

  3. rnaseq rnaseq Public

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

    Nextflow 794 663

  4. sarek sarek Public

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

    Nextflow 345 379

  5. chipseq chipseq Public

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

    Nextflow 174 141

  6. eager eager Public

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

    Nextflow 123 75

Repositories

Showing 10 of 130 repositories
  • modules Public

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

    Nextflow 256 MIT 644 396 (1 issue needs help) 150 Updated Jun 3, 2024
  • proteinfold Public

    Protein 3D structure prediction pipeline

    Nextflow 41 MIT 27 6 1 Updated Jun 3, 2024
  • circrna Public

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

    Nextflow 40 MIT 19 10 3 Updated Jun 3, 2024
  • raredisease Public

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

    Nextflow 74 MIT 34 23 1 Updated Jun 3, 2024
  • scrnaseq Public

    A single-cell RNAseq pipeline for 10X genomics data

    Nextflow 173 MIT 149 38 (1 issue needs help) 1 Updated Jun 3, 2024
  • crisprseq Public

    A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

    Nextflow 22 MIT 20 15 2 Updated Jun 3, 2024
  • createpanelrefs Public

    Generate Panel of Normals, models or other similar references from lots of samples

    Nextflow 4 MIT 5 4 2 Updated Jun 3, 2024
  • rnavar Public

    gatk4 RNA variant calling pipeline

    Nextflow 31 MIT 29 35 3 Updated Jun 3, 2024
  • tools Public

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

    Python 216 MIT 178 234 33 Updated Jun 3, 2024
  • oncoanalyser Public

    A comprehensive cancer DNA/RNA analysis and reporting pipeline

    Nextflow 15 MIT 2 2 1 Updated Jun 3, 2024
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