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Bioconductor

skill-leolin990405-r-analytics-skill-bioconductor · by LeoLin990405

R Bioconductor ecosystem for bioinformatics. Use for genomics, proteomics, and bioinformatics analysis.

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Install

$ agentstack add skill-leolin990405-r-analytics-skill-bioconductor

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

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About

Bioconductor

Open source software for bioinformatics.

Installation

# Install BiocManager
install.packages("BiocManager")

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

# Check version
BiocManager::version()

# Update packages
BiocManager::install()

Core Packages

# Genomic ranges
library(GenomicRanges)
library(IRanges)

# Sequences
library(Biostrings)

# Annotations
library(AnnotationDbi)
library(org.Hs.eg.db)

# RNA-seq
library(DESeq2)
library(edgeR)

GenomicRanges

library(GenomicRanges)

# Create GRanges
gr <- GRanges(
  seqnames = c("chr1", "chr1", "chr2"),
  ranges = IRanges(start = c(1, 100, 200), end = c(50, 150, 250)),
  strand = c("+", "-", "+")
)

# Operations
findOverlaps(gr1, gr2)
subsetByOverlaps(gr1, gr2)
reduce(gr)

Biostrings

library(Biostrings)

# DNA sequences
dna <- DNAString("ATCGATCG")
reverseComplement(dna)
translate(dna)

# Pattern matching
matchPattern("ATG", dna)
vmatchPattern("ATG", dna_set)

Annotation

library(org.Hs.eg.db)

# Map gene IDs
mapIds(org.Hs.eg.db,
  keys = gene_ids,
  column = "SYMBOL",
  keytype = "ENTREZID")

# Available columns
columns(org.Hs.eg.db)
keytypes(org.Hs.eg.db)

SummarizedExperiment

library(SummarizedExperiment)

# Create
se <- SummarizedExperiment(
  assays = list(counts = count_matrix),
  colData = sample_info,
  rowData = gene_info
)

# Access
assay(se)
colData(se)
rowData(se)

Finding Packages

# Search for packages
BiocManager::available("RNA")

# Package info
BiocManager::install("BiocPkgTools")
library(BiocPkgTools)
biocPkgList()

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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