A set of R packages and guidance for bioinformatics, the use of computing to study biological data such as genes, RNA, proteins, and evolutionary relationships.

Use it for genomic data analysis, RNA-seq studies, phylogenetic trees, mixed-effects models, and biological plots in R.

It brings related tools for genomic analysis, RNA sequencing, phylogenetics, statistics, and visualisation into one workflow.

r-bio — Skill for Claude Code and Codex by LeoLin990405

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 LeoLin990405/r-analytics-skill --skill r-bio

Clone the repo

git clone --depth 1 https://github.com/LeoLin990405/r-analytics-skill

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-bio/github.svg)](https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio)

Your own site

<a href="https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-bio/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/leolin990405/r-analytics-skill/r-bio"><img src="https://agentmods.dev/badge/skills/leolin990405/r-analytics-skill/r-bio.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 29 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,138 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 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.

Model	Per session	Once invoked
Fable 5.1	$0.00029	$0.01138
Opus 5.5	$0.00012	$0.00455
Sonnet 5.5	$0.00006	$0.00228
Haiku 4.5	$0.00003	$0.00114

Measured 1mo ago against content hash b0c8d79a5e06, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

r-bio 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 1mo 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.

sub-skills/r-bio/SKILL.md · 171 lines

How it starts

The opening of the file, as written. The whole thing — 171 lines — stays where its author put it; the contents beside it link to each section on GitHub.

R Bioinformatics Skill

Sub-skills

Sub-skill	Description
r-bio-genomics	GenomicRanges, Biostrings, annotation
r-bio-rnaseq	DESeq2, edgeR, differential expression
r-bio-phylo	ape, ggtree, phylogenetics

Bioinformatics and biostatistics in R.

Core Packages

Package	Description
Bioconductor ★	Genomic data analysis platform
GenomicRanges	Genomic intervals
Biostrings	DNA/RNA/protein sequences
SummarizedExperiment	Assay data container

Genetics & Phylogenetics

Package	Description
genetics	Genetic data handling
gap	Genetic data analysis
ape	Phylogenetics and evolution
ggtree	Phylogenetic tree visualization

Mixed Effects (Biostatistics)

Package	Description
lme4 ★	Mixed-effects models
nlme	Mixed-effects with custom covariance
glmmTMB	Generalized mixed-effects

Visualization

Package	Description
pheatmap	Pretty heatmaps
ComplexHeatmap	Advanced heatmaps
EnhancedVolcano	Volcano plots

Quick Examples

# Install Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

# Install packages
BiocManager::install(c("DESeq2", "edgeR", "GenomicRanges"))

# GenomicRanges
library(GenomicRanges)
gr <- GRanges(
  seqnames = c("chr1", "chr1", "chr2"),
  ranges = IRanges(start = c(100, 200, 150), width = 50),
  strand = c("+", "-", "+"),
  score = c(1.5, 2.0, 3.0)
)
findOverlaps(gr1, gr2)
subsetByOverlaps(gr1, gr2)

# RNA-seq with DESeq2
library(DESeq2)
dds <- DESeqDataSetFromMatrix(
  countData = counts,
  colData = sample_info,
  design = ~ condition
)
dds <- DESeq(dds)
res <- results(dds, contrast = c("condition", "treated", "control"))
sig <- res[which(res$padj < 0.05), ]

# Volcano plot
library(EnhancedVolcano)
EnhancedVolcano(res,
  lab = rownames(res),
  x = 'log2FoldChange',
  y = 'pvalue',
  pCutoff = 0.05,
  FCcutoff = 1
)

# Heatmap
library(pheatmap)
pheatmap(mat,
  scale = "row",
  clustering_distance_rows = "correlation",
  annotation_col = annotation
)

# Phylogenetic analysis
library(ape)
tree <- read.tree("tree.nwk")
plot(tree)

# Gene annotation
library(org.Hs.eg.db)
mapIds(org.Hs.eg.db,
  keys = gene_ids,
  column = "SYMBOL",
  keytype = "ENSEMBL"
)

Read the full file on GitHub · 171 lines

Files

What ships with it

17 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.

1mo ago First seen · 171 lines · 29 tokens per session scan A b0c8d79a5e06

Subscribe to this mod's changes

r-bio is a skill published in the GitHub repository LeoLin990405/r-analytics-skill (5 stars, last pushed 7mo ago), licensed MIT. It adds 29 tokens to every session and 1,138 once invoked, about $0.0001 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 2026-08-31.

Analytics and metrics Claude Code Scientific claude-code-skill claude-skill data-science r

foundations-mathematical-statistics

Choose and verify classical statistical tests from first principles — test-selection table with assumptions and exact/asymptotic null distributions, tie corrections, correct scipy.stats calls (binomtest, wilcoxon, mannwhitneyu, kruskal, kstest, chisquare ddof, chi2contingency, levene, ttestind equalvar=False), CI…

Pavel-Kravchenko/Bioinformatics · 131 tokens

r-bio