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    109 repositories

    • 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
      •
      MIT License
      •49•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • circrna

      Public
      circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
      Nextflow
      •
      MIT License
      •27•0•0•0•Updated Nov 25, 2024Nov 25, 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
      •
      MIT License
      •27•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • methylseq

      Public
      Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
      Nextflow
      •
      MIT License
      •147•0•0•1•Updated Nov 8, 2024Nov 8, 2024

    • chipseq

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      •
      MIT License
      •149•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •719•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • airrflow

      Public
      B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
      Nextflow
      •
      MIT License
      •38•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •421•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • hic

      Public
      Analysis of Chromosome Conformation Capture data (Hi-C)
      Python
      •
      MIT License
      •57•0•0•0•Updated Oct 13, 2024Oct 13, 2024

    • spatialvi

      Public
      Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
      Nextflow
      •
      MIT License
      •20•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • atacseq

      Public
      ATAC-seq peak-calling and QC analysis pipeline
      Nextflow
      •
      MIT License
      •124•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •83•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      •
      MIT License
      •123•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •178•0•0•1•Updated Sep 30, 2024Sep 30, 2024

    • bacass

      Public
      Simple bacterial assembly and annotation pipeline
      Nextflow
      •
      MIT License
      •43•0•0•0•Updated Sep 14, 2024Sep 14, 2024

    • mag

      Public
      Assembly and binning of metagenomes
      Nextflow
      •
      MIT License
      •115•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • fetchngs

      Public
      Pipeline to fetch metadata and raw FastQ files from public databases
      Nextflow
      •
      MIT License
      •75•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • proteinfold

      Public
      Protein 3D structure prediction pipeline
      Nextflow
      •
      MIT License
      •45•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • rnafusion

      Public
      RNA-seq analysis pipeline for detection of gene-fusions
      Nextflow
      •
      MIT License
      •99•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • diaproteomics

      Public
      Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
      Nextflow
      •
      MIT License
      •13•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • cageseq

      Public
      CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
      Nextflow
      •
      MIT License
      •13•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • pgdb

      Public
      The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
      Nextflow
      •
      MIT License
      •11•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • reportho

      Public
      nf-core pipeline for comparative analysis of ortholog predictions
      Nextflow
      •
      MIT License
      •5•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • dualrnaseq

      Public
      Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
      Nextflow
      •
      MIT License
      •33•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • molkart

      Public
      A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
      Nextflow
      •
      MIT License
      •9•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • viralintegration

      Public
      Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
      Python
      •
      MIT License
      •9•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • proteomicslfq

      Public
      Proteomics label-free quantification (LFQ) analysis pipeline
      Nextflow
      •
      MIT License
      •20•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • metaboigniter

      Public
      Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
      Nextflow
      •
      MIT License
      •16•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • readsimulator

      Public
      A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
      Nextflow
      •
      MIT License
      •7•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • quantms

      Public
      Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
      Nextflow
      •
      MIT License
      •39•0•0•0•Updated Jun 18, 2024Jun 18, 2024