bio-hi-c-analysis-hic-data-io
Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-data-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: cooler 0.9+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Hi-C Data I/O **"Load my Hi-C contact matrix"** → Read .cool/.mcool/.hic files into Python, access contact pixels, convert between formats, and export subsets. - Python: `cooler.Cooler('file.mcool::resolutions/10000')` - CLI: `cooler load`, `hic2cool convert` Load and manipulate Hi-C contact matrices in cooler format. ## Required Imports ```python import cooler import numpy as np import pandas as pd ``` ## Load a Cooler File ```python # Load a .cool file clr = cooler.Cooler('matrix.cool') # Basic info print(f'Chromosomes: {clr.chromnames}') print(f'Bin size: {clr.binsize}') print(f'Number of bins: {clr.info["nbins"]}') print(f'Sum of counts: {clr.info["sum"]}') ``` ## Load Multi-Reso
- Version Compatibility
- Required Imports
- Load a Cooler File
- Load Multi-Resolution Cooler (.mcool)
- Access Bin Information
- Access Pixel (Contact) Information
- Extract Contact Matrix
- Extract Submatrix (Two Regions)
- Convert from .hic to Cooler
- Convert from Text Formats
- Create Cooler from Matrix
- Merge Cooler Files
- Coarsen Resolution
- Export to Other Formats
Using hic2cool CLI hic2cool convert input.hic output.mcool -r 0 # All resolutions Specific resolution hic2cool convert input.hic output.cool -r 10000 Using cooler dump cooler dump -t pixels --join matrix.cool > pairs.txt Dump bins cooler dump -t bins matrix.cool > bins.txt
What does the bio-hi-c-analysis-hic-data-io skill do?
Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-data-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.