cutandrun

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

An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

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

Peak calling optimization via real time results assessment and interactive parameter adjustment.

Articles and Computational Methods for CUT&RUN and CUT&Tag

Enhancer Network Explorer is an interactive Shiny application designed to visualize and explore transcriptional regulatory networks between Transcription Factors (TFs), Enhancers, and Target Genes.

Slurm-first CUT&RUN/CUT&Tag workflow with spike-in normalization, SEACR peak calling, optional deepTools post-processing, and an nf-core wrapper