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.
npx agentmods add skills/thesecondfox/skill/bio-data-visualization-upset-plotsnpx skills add thesecondfox/skill --skill bio-data-visualization-upset-plotsgit clone --depth 1 https://github.com/thesecondfox/skillWrote 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.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-data-visualization-upset-plots)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-data-visualization-upset-plots"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-data-visualization-upset-plots.svg" alt="Measured on agentmods" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00053 | $0.01799 |
| Opus 5 | $0.00026 | $0.00899 |
| Sonnet 5 | $0.00011 | $0.00360 |
| Haiku 4.5 | $0.00005 | $0.00180 |
Grade A, and why
bio-data-visualization-upset-plots 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 3d 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.
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.
How it starts
The opening of the file, as written. The whole thing — 228 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: matplotlib 3.8+, pandas 2.2+, scanpy 1.10+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_nameto verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
UpSet Plots
"Visualize set intersections" → Replace Venn diagrams with UpSet plots for comparing overlaps across many gene/peak/variant sets.
- R:
UpSetR::upset(fromList(sets)) - Python:
upsetplot.UpSet.from_memberships()orfrom_indicators()
UpSetR (R) - Basic Plot
library(UpSetR)
# From binary matrix (rows = elements, columns = sets)
upset(fromExpression(data), order.by = 'freq', nsets = 6)
# From list of sets
gene_sets <- list(
SetA = c('Gene1', 'Gene2', 'Gene3', 'Gene4'),
SetB = c('Gene2', 'Gene3', 'Gene5', 'Gene6'),
SetC = c('Gene1', 'Gene3', 'Gene6', 'Gene7'),
SetD = c('Gene3', 'Gene4', 'Gene7', 'Gene8')
)
upset(fromList(gene_sets), order.by = 'freq', nsets = 4)
UpSetR Customization
# Customized appearance
upset(fromList(gene_sets),
nsets = 6,
nintersects = 40,
order.by = 'freq',
decreasing = TRUE,
mb.ratio = c(0.6, 0.4), # Matrix to bar ratio
point.size = 3,
line.size = 1.5,
mainbar.y.label = 'Intersection Size',
sets.x.label = 'Set Size',
text.scale = c(1.5, 1.3, 1.3, 1, 1.5, 1.3),
set_size.show = TRUE,
set_size.scale_max = 500)
# Custom set colors
upset(fromList(gene_sets),
sets.bar.color = c('#E64B35', '#4DBBD5', '#00A087', '#3C5488'),
main.bar.color = '#7E6148',
matrix.color = '#7E6148')
UpSetR with Queries
Goal: Highlight specific set intersections of interest within an UpSet plot.
Approach: Define query lists specifying which set combinations to highlight, assigning each a distinct color, so they stand out against the default bars.
What ships with it
1 file 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.
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.
- 3d ago First seen · 228 lines · 53 tokens per session scan A 3e0757ba1548
bio-data-visualization-upset-plots is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 53 tokens to every session and 1,799 once invoked, about $0.0003 per session on Opus 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 2026-08-31.
Other skills, from other repositories
systematic-debugging
Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes.
brainstorming
You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.
auto-perf-optimize
Run agent-driven VS Code performance or memory investigations. Use when asked to launch Code OSS, automate a VS Code scenario, run the Chat memory smoke runner, capture renderer heap snapshots, take workflow screenshots, compare run summaries, or drive a repeatable scenario before heap-snapshot analysis.
chat-perf
Run chat perf benchmarks and memory leak checks against the local dev build or any published VS Code version. Use when investigating chat rendering regressions, validating perf-sensitive changes to chat UI, or checking for memory leaks in the chat response pipeline.
chat-pet-sprite-creation
Use when creating or changing VS Code chat pet sprite art, sprite sheets, state animations, eye treatments, Stable/Insiders variants, or pet transitions under src/vs/workbench/contrib/chat/browser/widget/media/chatPet.
cpu-profile-analysis
Analyze V8/Chrome CPU profiles (.cpuprofile) and DevTools trace files (Trace-.json). Use when: profiling performance, investigating slow functions, comparing code paths, finding bottlenecks, analyzing timeToRequest, understanding call trees from sampling profiler data, analyzing layout/paint/rendering, investigating…