tangermeme

tangermeme is a skill for Claude Code, Codex from jmschrei/tangermeme. It costs 147 tokens per session (1,179 once invoked), scanned A, original, MIT.

A toolkit for analyzing genomic sequence-to-function models after training. It helps inspect what DNA patterns a model learned and test how changing a sequence affects its output.

In plain words
What is it for?
Use it for predictions, DeepLIFT or SHAP explanations, motif removal and spacing tests, saturation mutagenesis, variant-effect scoring, sequence design, and seqlet calling.
Why use it?
It gives you common ways to study model predictions and explanations without tying the work to one model type or DNA alphabet. This reduces the need to build separate code for each experiment.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it for predictions, DeepLIFT or SHAP explanations, motif removal and spacing tests, saturation mutagenesis, variant-effect scoring, sequence design, and seqlet calling.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jmschrei/tangermeme/data
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 jmschrei/tangermeme --skill data
Clone the repo
git clone --depth 1 https://github.com/jmschrei/tangermeme

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 tangermeme

README.md
[![agentmods](https://agentmods.dev/badge/skills/jmschrei/tangermeme/data/github.svg)](https://agentmods.dev/skills/jmschrei/tangermeme/data)
Your own site
<a href="https://agentmods.dev/skills/jmschrei/tangermeme/data"><img src="https://agentmods.dev/badge/skills/jmschrei/tangermeme/data/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 tangermeme

Your own site · 80×15
<a href="https://agentmods.dev/skills/jmschrei/tangermeme/data"><img src="https://agentmods.dev/badge/skills/jmschrei/tangermeme/data.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 147 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,179 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. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original 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 $0.00147 $0.01179
Opus 5.5 $0.00059 $0.00472
Sonnet 5.5 $0.00029 $0.00236
Haiku 4.5 $0.00015 $0.00118

Measured 4d ago against content hash 5353746af945, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

tangermeme 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 4d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/audit_deeplift.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.

tangermeme/_skills/data/SKILL.md · 62 lines

How it starts

The opening of the file, as written. The whole thing — 62 lines — stays where its author put it; the contents beside it link to each section on GitHub.

tangermeme

Post-training analysis of any PyTorch sequence model: batched prediction, attribution, perturbation experiments, sequence design, on raw outputs with no distance baked in. This file routes; the reference files hold the signatures, defaults and silent failures. Read the file for the task before writing code: several defaults select the wrong output, return a variable number of objects, or run zero iterations without a word.

Task to reference file

task read
attribution via DeepLIFT/SHAP: which bases drive this prediction, logos, hypothetical scores for CWMs, references, memory references/deep_lift_shap.md
a convergence delta warning, a transformer, attention pooling, a functional softmax or product, a custom module, "are these attributions correct" references/deep_lift_shap-unhooked-ops.md and scripts/audit_deeplift.py
ISM / saturation mutagenesis, fast=True references/saturation_mutagenesis.md
saliency (input x gradient, one backward pass) and dependency maps (epistasis, motif-flank interactions) references/dependency_map.md
PISA: attribution of every output position references/pisa.md
effect of a motif or region: marginalize, ablate, spacing; choosing backgrounds references/motif-effects.md
variant effects from a VCF: substitution, deletion, insertion references/variant-effect.md
seqlets from attributions, choosing a threshold with a control references/seqlets.md
motif labels and counts: TOMTOM, co-occurrence, spacing references/annotate.md
logos with seqlet or motif annotations references/plot.md
a function over a product of inputs (sequence x cell state x depth) references/product.md
composing predict / attribution through a perturbation (func=, additional_func_kwargs, args=) references/func-pattern.md
a model with several inputs or outputs, a profile head, a control track; N models in one sweep references/model-wrapping.md
loading loci, FASTA, bigWig, MEME, VCF; GC-matched background loci; window to genome coordinates references/io-loci.md
editing sequences: insert, substitute, delete, shuffle, random draws, reverse complement, one-hot, PackedSequence references/ersatz.md
designing sequences to a target output: screen, greedy, beam references/design.md

Read the full file on GitHub · 62 lines

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. 4d ago Changed · -37 lines · +20 tokens per session 5353746af945
  2. 5d ago Changed · +4 lines c6470452a5f0
  3. 11d ago Changed a56271b90e7c
  4. 12d ago Changed · +1 lines 0e7efe837607
  5. 21d ago Changed ca7574e7854c
  6. 24d ago Changed · +2 lines e3f05c0e73c4
  7. 29d ago Changed · +2 lines 39eab7a84476
  8. 1mo ago Changed b79c5b91d0e3
  9. 1mo ago First seen · 90 lines · 127 tokens per session scan A e8b7311cee6b

Subscribe to this mod's changes

tangermeme is a skill published in the GitHub repository jmschrei/tangermeme (329 stars, last pushed 3d ago), licensed MIT. It adds 147 tokens to every session and 1,179 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 2026-08-30.

Related

Other skills, from other repositories

arboreto

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.

K-Dense-AI/scientific-agent-skills · 55 tokens

deepspot-m

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 tiles at about 20x, querying the released protein-coding gene panel by symbol, and whole-slide prediction after resolution-aware tiling with histolab.

K-Dense-AI/scientific-agent-skills · 70 tokens

torchdrug

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and knowledge graph reasoning. Use when code imports torchdrug or needs its datasets, models, tasks, or Engine.

K-Dense-AI/scientific-agent-skills · 64 tokens

pyhealth

Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV, eICU or OMOP prediction tasks, patient-level evaluation, mortality/readmission/length-of-stay modeling, medication recommendation, sleep staging, Trainer…

K-Dense-AI/scientific-agent-skills · 84 tokens

ml-training-recipes

Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics. Covers training loops, optimizer selection (AdamW, Muon), LR scheduling, mixed precision, debugging, and systematic experimentation. Use when training or fine-tuning…

Orchestra-Research/AI-Research-SKILLs · 88 tokens

nemo-mbridge-perf-expert-parallel-overlap

Validate and use MoE expert-parallel communication overlap in Megatron-Bridge, including overlapmoeexpertparallelcomm, delaywgradcompute, and flex dispatcher backends such as DeepEP and HybridEP.

NVIDIA/skills · 56 tokens