atac-seq-analysis

atac-seq-analysis is a skill for Claude Code, Codex from Pavel-Kravchenko/Bioinformatics. It costs 83 tokens per session (2,292 once invoked), scanned A, original, no licence file.

A guide to analyzing ATAC-seq data, a sequencing method that shows which parts of DNA are accessible inside cells. It covers data quality checks, insertion-bias correction, nucleosome-free regions, and transcription-factor footprints.

In plain words
What is it for?
Use it to analyze BAM or BED files, measure fragment-size and nucleosome-free-region quality, correct Tn5 insertion offsets, and score footprints around DNA motifs.
Why use it?
It helps turn raw alignment files into checks and measurements that show whether the experiment worked and where regulatory proteins may bind DNA.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to analyze BAM or BED files, measure fragment-size and nucleosome-free-region quality, correct Tn5 insertion offsets, and score footprints around DNA motifs.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/pavel-kravchenko/bioinformatics/atac-seq-analysis
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Pavel-Kravchenko/Bioinformatics --skill atac-seq-analysis
Clone the repo
git clone --depth 1 https://github.com/Pavel-Kravchenko/Bioinformatics

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for atac-seq-analysis

README.md
[![agentmods](https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis/github.svg)](https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis)
Your own site
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for atac-seq-analysis

Your own site · 80×15
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/atac-seq-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 83 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,292 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00083 $0.02292
Opus 5 $0.00042 $0.01146
Sonnet 5 $0.00017 $0.00458
Haiku 4.5 $0.00008 $0.00229

Measured 9d ago against content hash 135802cf9414, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

atac-seq-analysis scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

for read in bam.fetch(chrom, start, end):
Skills/atac-seq-analysis/SKILL.md · 184 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 184 lines · 83 tokens per session scan A 135802cf9414

Subscribe to this mod's changes

atac-seq-analysis is a skill published in the GitHub repository Pavel-Kravchenko/Bioinformatics (5 stars, last pushed 2mo ago), with no licence file. It adds 83 tokens to every session and 2,292 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.