deeptools

80 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

By anubhavg-icpl/vibe (GitHub) · coding · 13 stars · scanned at commit d51e7ac

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. Use when you need help with deeptools.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this. Expected for a coding skill.

Found in 77 places.

skills/sci-deeptools/SKILL.md, line 42python scripts/validate_files.py --bam sample1.bam sample2.bam --bed regions.bed
skills/sci-deeptools/SKILL.md, line 53python scripts/workflow_generator.py --list
skills/sci-deeptools/SKILL.md, line 72uv pip install deeptools

Show 17 more

skills/sci-deeptools/SKILL.md, line 145bamCoverage --bam input.bam --outFileName output.bw \
skills/sci-deeptools/SKILL.md, line 152bamCompare -b1 treatment.bam -b2 control.bam -o ratio.bw \
skills/sci-deeptools/SKILL.md, line 164plotFingerprint -b input.bam chip.bam -o fingerprint.png \
skills/sci-deeptools/SKILL.md, line 170multiBamSummary bins --bamfiles *.bam -o counts.npz
skills/sci-deeptools/SKILL.md, line 184computeMatrix reference-point -S signal.bw -R genes.bed \
skills/sci-deeptools/SKILL.md, line 194plotProfile -m matrix.gz -o profile.png \
skills/sci-deeptools/SKILL.md, line 305samtools index input.bam
skills/sci-deeptools/SKILL.md, line 311bamCoverage --bam input.bam -o chr1.bw --region chr1
skills/sci-deeptools/SKILL.md, line 324python scripts/validate_files.py --bam *.bam --bed regions.bed
skills/sci-deeptools/SKILL.md, line 389python scripts/validate_files.py --bam sample1.bam sample2.bam \
skills/sci-deeptools/SKILL.md, line 408python scripts/workflow_generator.py --list
skills/sci-deeptools/SKILL.md, line 481grep -A 20 "^### toolname" references/tools_reference.md
.claude/settings.json, line 9"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-bash'",
.claude/settings.json, line 19"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-edit'",
.claude/settings.json, line 31"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-edit'",
.claude/settings.json, line 41"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-bash'",
.claude/settings.json, line 52"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" route'",

and 57 more places

Downloads and installs other software

The author does not mention this. It runs automatically when the plugin is installed.

Found in 11 places.

skills/sci-deeptools/SKILL.md, line 72uv pip install deeptools
.claude/settings.json, line 166"Bash(npx @claude-flow*)",
.claude/settings.json, line 167"Bash(npx claude-flow*)",

Show 8 more

.mcp.json, line 4"command": "npx",
hooks/cmods/README.md, line 96npx eslint --fix "$FILE" 2>/dev/null
hooks/cmods/post-edit-format.sh, line 29npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 32npx biome format --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 80npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 86npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/pre-commit-lint.sh, line 38echo "$files" | xargs npx eslint --max-warnings 0 2>/dev/null
hooks/hooks.json, line 106"command": "#!/bin/bash\n# Run TypeScript check after editing TS files\ninput=$(cat)\nfile_path=$(echo \"$input\" | jq -r '.tool_input.file_path // \"\"')\n\nif

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'deeptools' ] || [ -L ~/.agents/skills/'deeptools' ]; then echo 'A skill folder named deeptools already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/anubhavg-icpl/vibe' "$d" && git -C "$d" checkout --quiet 'd51e7ac9a34111cd2e63daed83c2198f91570050' -- 'skills/sci-deeptools' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sci-deeptools' ~/.agents/skills/'deeptools' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'deeptools' ~/.claude/skills/'deeptools' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-08	`d51e7ac`	80