Alterlab Deeptools

AlterLab Creative Technologies Laboratory

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile).

Install

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-deeptools

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-deeptools -a claude-code -g

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-deeptools -a codex -g

gemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-deeptools

gh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-deeptools

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-deeptools ~/.claude/skills/alterlab-deeptools   # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-deeptools ~/.agents/skills/alterlab-deeptools   # Codex, Cursor, Gemini CLI, Copilot, OpenCode

Install

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