Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
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Jul 27, 2026 - Nextflow
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cutandrun
Here are 8 public repositories matching this topic...
An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).
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Apr 28, 2026 - R
CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.
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Apr 5, 2022 - Nextflow
Reproducible Snakemake workflow for paired-end CUT&RUN (no spike-in): MACS2 + SEACR peak calling with matched IgG/Input controls, mode-aware consensus count matrices, ENCODE-grade QC, and opt-in DESeq2 differential binding + ChIPseeker/HOMER downstream analysis
quality-control snakemake homer epigenomics peak-calling deeptools cutandrun differential-binding chipseeker seacr motif-enrichment
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Jul 30, 2026 - Python
Articles and Computational Methods for CUT&RUN and CUT&Tag
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Oct 31, 2025
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Jan 13, 2025 - Python
Enhancer Network Explorer is an interactive Shiny application designed to visualize and explore transcriptional regulatory networks between Transcription Factors (TFs), Enhancers, and Target Genes.
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Jul 21, 2026 - R
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