bio-fragment-analysis

75 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By lilinji/GeneTind-Life-Skills (GitHub) · coding · 17 stars · scanned at commit 908229c

Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; D…

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this.

Found in 3 places.

skills/bio-fragment-analysis/SKILL.md, line 19Notes specific to this skill: FinaleToolkit CLI subcommands are hyphenated (`frag-length-bins`, `end-motifs`, `delfi-gc-correct`); the Python functions are unde
skills/bio-fragment-analysis/SKILL.md, line 163| `pip install delfi` fails / no DELFI CLI | DELFI is a method + company, not a package | Compute DELFI features via FinaleToolkit `delfi`, or a custom binned r
skills/bio-fragment-analysis/usage-guide.md, line 8pip install finaletoolkit pysam numpy pandas matplotlib

Connects to the internet

The author does not mention this.

Found in 5 places.

skills/bio-fragment-analysis/SKILL.md, line 79for read in bam.fetch(chrom):
skills/bio-fragment-analysis/examples/fragment_analysis.py, line 26sizes = [r.template_length for r in bam.fetch()
skills/bio-fragment-analysis/examples/fragment_analysis.py, line 50for read in bam.fetch(chrom):

Show 2 more

skills/bio-fragment-analysis/examples/fragment_analysis.py, line 71kept = sum(1 for r in bam.fetch()
skills/bio-fragment-analysis/examples/fragment_analysis.py, line 73total = sum(1 for r in bam.fetch()

Runs commands on your computer

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

Found in 2 places.

skills/bio-fragment-analysis/SKILL.md, line 104finaletoolkit delfi sample.bam hg38.chrom.sizes hg38.fa bins_100kb.bed -g gaps.bed -R -o sample.delfi.bed
skills/bio-fragment-analysis/SKILL.md, line 124snakemake -s griffin_genome_GC_frequency/griffin_genome_GC_frequency.snakefile --cores 8

Safer alternatives

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Install

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

if [ -e ~/.agents/skills/'bio-fragment-analysis' ] || [ -L ~/.agents/skills/'bio-fragment-analysis' ]; then echo 'A skill folder named bio-fragment-analysis already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-fragment-analysis' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-fragment-analysis' ~/.agents/skills/'bio-fragment-analysis' && 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/'bio-fragment-analysis' ~/.claude/skills/'bio-fragment-analysis' (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
2026-11-11	`908229c`	75