deeptools-ngs-analysis SKILL.md skillA
deeptools-ngs-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/deeptools-ngs-analysis@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/interval-ops/deeptools-ngs-analysis/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 16,339 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# deepTools — NGS Data Analysis Toolkit ## Overview deepTools is a command-line toolkit for processing and visualizing high-throughput sequencing data. It converts BAM alignments to normalized coverage tracks (bigWig), performs quality control (correlation, PCA, fingerprint), and generates publication-quality heatmaps and profile plots around genomic features. Supports ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq. ## When to Use - Converting BAM files to normalized bigWig coverage tracks - Comparing ChIP-seq treatment vs input control (log2 ratio tracks) - Assessing sample quality: replicate correlation, PCA, coverage depth - Evaluating ChIP enrichment strength (fingerprint plots) - Creating heatmaps and profile plots around TSS, peaks, or other genomic regions - Analyzing ATAC-seq data with Tn5 offset correction - Generating strand-specific RNA-seq coverage tracks - Use **omics-plotting** SKILL for custom figures from exported score matrices; standard signal heatmaps/profiles use deeptools' own `plotHeatmap`/`plotProfile` - For **read alignment**, use STAR, BWA, or bowtie2 instead - For **peak calling**, use MACS2 or HOMER instead …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/deeptools-ngs-analysis@sha256:f2d0e3ebde279903The line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_nlebpdnkc5pbkkol)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 16,339 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 16,388 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 14,016 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 13,855 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16339 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_nlebpdnkc5pbkkol GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/deeptools-ngs-analysis GET https://markdownregistry.com/api/v1/blob/f2d0e3ebde279903248ccbef63be721705c8867d964d43ca75021cb91264f211
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.