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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 Public

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

    Python 163 112

  2. modules Public

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

    Nextflow 118 257

  3. rnaseq Public

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

    Nextflow 504 485

  4. chipseq Public

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

    Nextflow 125 103

  5. sarek Public

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

    Nextflow 189 260

  6. eager Public

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

    Nextflow 71 61

Repositories

  • demultiplex Public

    UNDER CONSTRUCTION: Demultiplexing pipeline for Illumina sequencing data

    Nextflow 11 MIT 5 10 1 Updated Sep 15, 2022
  • circrna Public

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

    Perl 19 MIT 7 3 3 Updated Sep 15, 2022
  • modules Public

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

    Nextflow 118 MIT 257 177 (6 issues need help) 74 Updated Sep 15, 2022
  • cutandrun Public

    Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

    Nextflow 30 MIT 16 10 1 Updated Sep 15, 2022
  • funcscan Public

    Screening of functional components and natural products from assembled contigs

    Nextflow 9 MIT 4 11 2 Updated Sep 15, 2022
  • raredisease Public

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

    Nextflow 22 MIT 13 24 4 Updated Sep 15, 2022
  • chipseq Public

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

    Nextflow 125 MIT 103 13 1 Updated Sep 15, 2022
  • tools Public

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

    Python 163 MIT 112 108 9 Updated Sep 15, 2022
  • airrflow Public

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

    Nextflow 19 MIT 13 5 3 Updated Sep 15, 2022
  • proteinfold Public

    UNDER CONSTRUCTION: Protein 3D structure prediction pipeline

    Nextflow 2 MIT 7 1 0 Updated Sep 15, 2022
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