deepTools NGS analysis: BAM to bigWig, QC, heatmaps and profiles for sequencing data
Full deepTools playbook for NGS — validate files, generate workflow scripts, normalize (RPGC/CPM/RPKM/BPM), run QC (fingerprint, correlation, PCA), convert BAM to coverage tracks, plot heatmaps and profiles around TSS/peaks
- What
- Full deepTools playbook for NGS — validate files, generate workflow scripts, normalize (RPGC/CPM/RPKM/BPM), run QC (fingerprint, correlation, PCA), convert BAM to coverage tracks, plot heatmaps and profiles around TSS/peaks
- Cost
- Free
- Needs
- deepTools installed (uv pip install deepTools or conda/bioconda); real sequencing data (BAM/BED/bigWig files) to analyze — the skill is a guided workflow, not software
- Install
- Copy the installer prompt below into your Muse — your agent does the rest.
Curated by Skill Harbor — @k-dense-ai's deepTools skill for next-generation sequencing analysis: a complete command-level playbook for ChIP-seq, RNA-seq, ATAC-seq and MNase-seq. Convert BAM alignments to normalized coverage tracks (bamCoverage), run QC (plotFingerprint, multiBamSummary correlation, plotPCA), compare samples (bamCompare with log2 normalization), and build heatmaps and profile plots around genomic features (computeMatrix → plotHeatmap/plotProfile). Includes a normalization-method selection guide (RPGC, CPM, RPKM, BPM — when each is valid), effective-genome-size tables for common organisms, best-practice rules (validate files first, never extend reads for RNA-seq, always for ChIP-seq), and two helper scripts: validate_files.py for input checking and a workflow generator that scaffolds full bash pipelines (chipseq_qc, chipseq_analysis, rnaseq_coverage, atacseq). Honest caveats: tooling plus methodology — deepTools must be installed (uv pip or conda/bioconda, especially on shared HPC) and you need real sequencing data (BAM/BED/bigWig); the bundled commands assume command-line workflows; the skill asks that substantial use be cited in manuscripts (arXiv:2609.00065). MIT licensed. Skill Harbor never reviews the code, review it yourself before use. Discovered via skills.sh.
Version:
Install
Prerequisites: deepTools installed (uv pip install deepTools or conda/bioconda); real sequencing data (BAM/BED/bigWig files) to analyze — the skill is a guided workflow, not software Install "deepTools NGS analysis: BAM to bigWig, QC, heatmaps and profiles for sequencing data" for me. It gives my agent @k-dense-ai's deepTools playbook: validate input files, generate ready-to-run workflow scripts (ChIP-seq QC/analysis, RNA-seq coverage, ATAC-seq), pick the right normalization (RPGC/CPM/RPKM/BPM) with effective genome sizes, run QC and sample comparison, convert BAM to coverage tracks, and plot heatmaps/profiles — with best-practice rules for each assay type. MIT-licensed. Repository: https://github.com/k-dense-ai/scientific-agent-skills/blob/main/skills/deeptools/SKILL.md 1. Fetch the SKILL.md file (and any helper files) from the repository path into a temporary folder and summarize what it does in one or two sentences. 2. Safety check: review the SKILL.md and scripts for anything suspicious (unexpected network calls, shell commands, credential harvesting). This repo should contain zero secrets in code, credentials only via the secure vault, allowed hosts declared in the SKILL.md. Verify that holds here; STOP on any red flag and tell me. 3. Install it as a skill: copy SKILL.md and its helper files into the agent's skills directory, in a folder named "deeptools". 4. Verify with no network calls: frontmatter valid, files in place. 5. Report what was installed, where, and what I still need to do myself (e.g. point the agent at my BAM/BED/bigWig files and the organism; cite the Scientific Agent Skills paper (arXiv:2609.00065) if it materially contributed to a manuscript). GitHub is optional: if I have a GitHub account or the gh CLI, you may use it; otherwise public access is fine. Never require it unless it's in the prerequisites above. Rules: don't touch anything outside the temp folder and the install target. If anything looks off, stop and ask me.
Questions
How do I install a build?
Every product page includes a copy-paste install prompt. Paste it into your Muse and it sets the build up for you — no manual configuration.
Where does my money go?
Straight to the seller. Skill Harbor never processes payments: checkout happens on the seller’s own page, usually Stripe.
What does the ✓ next to a creator’s name mean?
It means we confirmed the identity of the person behind the listing. It says nothing about the code itself — always check a build before installing it.