bio-hi-c-analysis-hic-data-io

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

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chrom…

Works with any agent that supports SKILL.md skills.

What this skill can do

Connects to the internet

The author does not mention this.

Found in 11 places.

skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 24- Python: `cooler.Cooler('file.mcool::/resolutions/10000').matrix(balance=True).fetch('chr1')`
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 60| `fetch('1')` returns empty on a `chr1` file | harmonize chrom naming first | chr1-vs-1 silently zeros every join, no error |
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 76`clr.matrix().fetch(region)` takes a UCSC region string or a bare chrom name; one arg -> symmetric square, two args -> rectangular submatrix (incl. trans). `clr

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skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 85balanced = clr.matrix(balance=True).fetch('chr1') # multiplicative cooler weight
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 86raw = clr.matrix(balance=False).fetch('chr1') # observed counts
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 87kr = clr.matrix(balance='KR').fetch('chr1') # KR/VC/VC_SQRT auto-treated as divisive by name
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 88sparse = clr.matrix(balance=True, sparse=True).fetch('chr1') # scipy COO for large chromosomes
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 145np.save('chr1.npy', clr.matrix(balance=True).fetch('chr1'))
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 156The bin table IS the identity of a cooler. Two coolers are pixel-comparable only if their bin tables are byte-identical: same chroms, same order, same contigs p
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 204| `fetch('1')` returns nothing | chr1-vs-1 naming mismatch | harmonize chrom naming across all inputs |
skills/bio-hi-c-analysis-hic-data-io/examples/load_cooler.py, line 26matrix = clr.matrix(balance=True).fetch('chr1') # cooler weight is multiplicative

Runs commands on your computer

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

Found in 3 places.

skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 94hic2cool convert in.hic out.mcool -r 0 # -r 0 = all resolutions -> .mcool; norm vectors un-inverted (>=0.5.0)
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 138cooler zoomify -r 10000,50000,100000,500000 --balance hires.cool # raw-coarsen then ICE afresh per level
skills/bio-hi-c-analysis-hic-data-io/SKILL.md, line 149cooler dump -t pixels --join --balanced in.cool > pixels.tsv # --balanced requires a balanced file

Downloads and installs other software

The author does not mention this.

Found in 1 place.

skills/bio-hi-c-analysis-hic-data-io/usage-guide.md, line 10pip install cooler hic2cool hictk bioframe numpy pandas

Safer alternatives

Low-risk skills in the same category (coding) that look related. Check that one does what you need.

Install

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

if [ -e ~/.agents/skills/'bio-hi-c-analysis-hic-data-io' ] || [ -L ~/.agents/skills/'bio-hi-c-analysis-hic-data-io' ]; then echo 'A skill folder named bio-hi-c-analysis-hic-data-io 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-hi-c-analysis-hic-data-io' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-hi-c-analysis-hic-data-io' ~/.agents/skills/'bio-hi-c-analysis-hic-data-io' && 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-hi-c-analysis-hic-data-io' ~/.claude/skills/'bio-hi-c-analysis-hic-data-io' (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