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pydeseq2

pydeseq2 is a skill for Claude Code from KalarisLabs/research-agent-skills. It costs 149 tokens per session (3,553 once invoked), scanned A, original, no licence file.

Runs differential expression analysis on bulk RNA-seq count data with PyDESeq2, the Python port of DESeq2. Covers formulaic single- and multi-factor designs, contrasts, Wald tests, Benjamini-Hochberg FDR correction, optional apeGLM LFC shrinkage, pandas and AnnData (H5AD) integration, CSV export, volcano and MA plots…

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

not rated 105repo today A scan 149 tokens custom licence
Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/kalarislabs/research-agent-skills/pydeseq2
View source ↗ KalarisLabs/research-agent-skills docs.kalarislabs.com
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 KalarisLabs/research-agent-skills --skill pydeseq2
Clone the repo
git clone --depth 1 https://github.com/KalarisLabs/research-agent-skills

Made for: Claude Code.

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 pydeseq2

README.md
[![agentmods](https://agentmods.dev/badge/skills/kalarislabs/research-agent-skills/pydeseq2/github.svg)](https://agentmods.dev/skills/kalarislabs/research-agent-skills/pydeseq2)
Your own site
<a href="https://agentmods.dev/skills/kalarislabs/research-agent-skills/pydeseq2"><img src="https://agentmods.dev/badge/skills/kalarislabs/research-agent-skills/pydeseq2/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 pydeseq2

Your own site · 80×15
<a href="https://agentmods.dev/skills/kalarislabs/research-agent-skills/pydeseq2"><img src="https://agentmods.dev/badge/skills/kalarislabs/research-agent-skills/pydeseq2.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 149 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,553 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. 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 $0.00149 $0.03553
Opus 5.5 $0.00060 $0.01421
Sonnet 5.5 $0.00030 $0.00711
Haiku 4.5 $0.00015 $0.00355

Measured today against content hash 7bde895be761, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

pydeseq2 scanned grade A with 0 findings 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 today.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/run_deseq2_analysis.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/pydeseq2/SKILL.md · 400 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. today First seen · 400 lines · 149 tokens per session scan A 7bde895be761

Subscribe to this mod's changes

pydeseq2 is a skill published in the GitHub repository KalarisLabs/research-agent-skills (105 stars, last pushed today), with no licence file. It adds 149 tokens to every session and 3,553 once invoked, about $0.0006 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-11-07.

Data and AIDocumentsTestingacademic-researchacademic-writingagent-skillsai-agentsbioinformaticscitation-verification
Related

pydeseq2 compared with skills from other repositories

pydeseq2 next to 6 skills from other repositories
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pydeseq2KalarisLabs/research-agent-skillsSkill105todaynoneA149Claude Code
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markitdownK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA62Claude Code, Codex
aamas-submissionbrycewang-stanford/Awesome-Journal-SkillsSkill1.4k1mo agoMITA79Claude Code
aejpol-replication-packagebrycewang-stanford/Awesome-Journal-SkillsSkill1.4k1mo agoMITA0Claude Code
aejmac-tables-figuresbrycewang-stanford/Awesome-Journal-SkillsSkill1.4k1mo agoMITA0Claude Code
aaai-artifact-evaluationbrycewang-stanford/Awesome-Journal-SkillsSkill1.4k1mo agoMITA47Claude Code