Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.
中文简介正在准备中。当前显示英语简介。
Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.
安装前可以查看交给 AI 代理的指令内容。
Use this skill as the epigenomics dispatcher for ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag analysis. Hand off to the assay-specific deep skill once the assay type is known.
Confirm:
Choose the workflow by assay:
ngs-atacseq-peaks-qc using nf-core/atacseq by defaultngs-chip-cutrun-peaks-qc using nf-core/chipseq by defaultngs-chip-cutrun-peaks-qc using nf-core/cutandrun by defaultUse direct MACS2 only for focused peak-calling tasks from prepared BAMs.
python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline epigenomics_peaks --emit-install-plan
For FASTQ intake/QC over ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag data, use the shared FASTQ assay package:
python plugins/ngs-analysis/scripts/run_fastq_assay_package.py \
--lane epigenomics_peaks \
--sample-sheet assay_samples.csv \
--execute
This validates sample-sheet paths and read structure, runs seqkit stats and FastQC/MultiQC when available, and writes peak_calling_readiness.json. Full alignment, signal tracks, TSS/FRiP, consensus peaks, and differential analyses still route through the assay-specific workflow.
Assay-specific ATAC and ChIP/CUT&RUN runners now also emit native review files alongside TSV/JSON summaries: qc/*_dashboard.html, FRiP/peak SVG plots, insert-size SVG plots, browser-track preview HTML, UCSC track lines, and IGV session files.
ATAC-seq preflight run:
nextflow run nf-core/atacseq \
-profile test,docker \
--outdir results/atacseq_test
ChIP-seq preflight run:
nextflow run nf-core/chipseq \
-profile test,docker \
--outdir results/chipseq_test
CUT&RUN/CUT&Tag preflight run:
nextflow run nf-core/cutandrun \
-profile test,docker \
--outdir results/cutandrun_test
Carry replicate and control metadata through the sample sheet before running real analysis.
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Review charts, diagrams, and dashboards for accessibility, including color contrast, keyboard access, and text alternatives. Get specific guidance for preserving key findings in screen readers, static exports, and reduced-motion views.
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Give a photo collection a consistent look using Adobe tools to adjust color, tone, presets, and optional crops. Review a before-and-after sample before processing the full set, then receive links to the edited images.
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Visualize a logo, sketch, or design on products such as mugs, shirts, and business cards. Review a pilot image, generate a visually consistent set, and collect the results on a shareable Firefly Board.
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Prepare images and videos for social platforms using Adobe tools. Create image crops that keep the subject in view, expand backgrounds when available, preview a full-set sample, and resize videos while preserving their aspect ratio.
中文简介正在准备中。当前显示英语简介。
Create flyers, social posts, business cards, and other visuals from Adobe Express templates. Choose a template, customize its text and background color, and receive a design link, with additional editing and export options depending on the available tools.
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Turn an uploaded video into three highlight edits with Adobe Quick Cut. Choose a target length and style, then compare versions that feature different moments and download the ones you prefer.
中文简介正在准备中。当前显示英语简介。