ReddRadar
Agent skill
bio-epitranscriptomics-modification-visualization
Install this agent skill to your Project
npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epitranscriptomics-modification-visualization
SKILL.md
name: bio-epitranscriptomics-modification-visualization description: Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons. tool_type: r primary_tool: Guitar measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:
- read_file
- run_shell_command
Modification Visualization
Metagene Plots with Guitar
library(Guitar)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
# Load m6A peaks
peaks <- import('m6a_peaks.bed')
# Create metagene plot
# Shows distribution relative to transcript features
GuitarPlot(
peaks,
txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
saveToPDFprefix = 'm6a_metagene'
)
Custom Metagene with deepTools
# Create bigWig from IP/Input ratio
bamCompare -b1 IP.bam -b2 Input.bam \
--scaleFactors 1:1 \
--ratio log2 \
-o IP_over_Input.bw
# Metagene around stop codons
computeMatrix scale-regions \
-S IP_over_Input.bw \
-R genes.bed \
--regionBodyLength 2000 \
-a 500 -b 500 \
-o matrix.gz
plotProfile -m matrix.gz -o metagene.pdf
Browser Tracks
# Create normalized bigWig for genome browser
bamCoverage -b IP.bam \
--normalizeUsing CPM \
-o IP_normalized.bw
# Peak BED to bigBed
bedToBigBed m6a_peaks.bed chrom.sizes m6a_peaks.bb
Heatmaps
library(ComplexHeatmap)
# m6A signal around peaks
Heatmap(
signal_matrix,
name = 'm6A signal',
cluster_rows = TRUE,
show_row_names = FALSE
)
Related Skills
- epitranscriptomics/m6a-peak-calling - Generate peaks for visualization
- data-visualization/genome-tracks - IGV, UCSC integration
- chip-seq/chipseq-visualization - Similar techniques
Recommended Agent Skills
Expand your agent's capabilities with these related and highly-rated skills.
FreedomIntelligence/OpenClaw-Medical-Skills
vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
FreedomIntelligence/OpenClaw-Medical-Skills
chemist-analyst
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.
FreedomIntelligence/OpenClaw-Medical-Skills
bio-alignment-io
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
FreedomIntelligence/OpenClaw-Medical-Skills
sleep-analyzer
分析睡眠数据、识别睡眠模式、评估睡眠质量，并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。
FreedomIntelligence/OpenClaw-Medical-Skills
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
FreedomIntelligence/OpenClaw-Medical-Skills
bio-hi-c-analysis-matrix-operations
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.
Didn't find tool you were looking for?