bio-hi-c-analysis-contact-pairs
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-contact-pairs --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+, pairtools 1.1+, pandas 2.2+ 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 Contact Pairs Processing **"Process my Hi-C read pairs"** → Parse aligned Hi-C reads into contact pairs, filter duplicates, classify pair types (cis/trans), and generate contact statistics. - CLI: `pairtools parse` → `pairtools sort` → `pairtools dedup` → `pairtools stats` Process Hi-C read pairs with pairtools. ## Pairtools Workflow Overview ``` BAM (aligned reads) | v pairtools parse (extract pairs) | v pairtools sort | v pairtools dedup (remove duplicates) | v pairtools select (filter by type) | v Valid pairs for matrix generation ``` ## Parse Alignments to Pairs ```bash # Parse BAM to pairs format pairtools parse \ --chroms-path chromsizes.txt \ --min-mapq 30 \ --walks-policy 5unique \ --output par
- Version Compatibility
- Pairtools Workflow Overview
- Parse Alignments to Pairs
- Sort Pairs
- Remove Duplicates
- View Pairs File
- Filter by Pair Type
- Filter by Distance
- Filter by MAPQ
- Generate Statistics
- Split by Pair Type
- Merge Pairs Files
- Generate Fragment Pairs (Restriction Sites)
- Convert to Different Formats
Parse BAM to pairs format pairtools parse \ aligned.bam With restriction enzyme cut sites aligned.bam | \ pairtools restrict -f enzyme_sites.bed | \ gzip > parsed.restricted.pairs.gz Sort pairs by position pairtools sort \ parsed.pairs.gz
What does the bio-hi-c-analysis-contact-pairs skill do?
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-contact-pairs --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.