bio-clip-seq-crosslink-site-detection
Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.
npx skills add BioTender-max/awesome-bio-agent-skills --skill crosslink-site-detection --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: PureCLIP 1.3.1+, CTK 1.1.4+, PARalyzer 1.5+, wavClusteR 2.34+, pyCRAC 1.5+, samtools 1.19+, bedtools 2.31+, pysam 0.22+, R 4.3+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws unexpected errors, introspect the installed tool and adapt the example to match the actual CLI rather than retrying. # CLIP-seq Crosslink-Site Detection **"Detect single-nucleotide crosslink sites in my CLIP data"** -> Identify the exact base where the protein-RNA UV adduct caused the reverse transcriptase to stop (truncation, in iCLIP/eCLIP), to read through with a mutation (deletion in HITS-CLIP, T->C in PAR-CLIP), or to leave a multi-base signature (PARalyzer kernel density for PAR-CLIP). Single-nucleotide resolution is the foundation of motif registration (mCross), allele-specific binding (BEAPR/ASPRIN), variant-effect prediction, and the most rigorous comparisons across CLIP variants. T
- Version Compatibility
- Crosslink Chemistry by CLIP Variant
- Algorithmic Taxonomy
- Critical Choice: Truncation vs Mutation vs HMM
- Per-Tool Failure Modes
- PureCLIP -- HMM convergence on sparse coverage
- PureCLIP -- Misses broad binding zones
- CITS truncation -- Misapplied to PAR-CLIP
- CIMS deletion -- Misapplied to iCLIP
- PARalyzer -- Parameter sensitivity
- Aligner deletion-tolerance for HITS-CLIP
- PAR-CLIP T->C mismatch ceiling
- Strand mis-assignment for truncation site
- Decision Tree by Use Case
Step 1: PureCLIP single-nt sites pureclip \ Step 2: mCross motif registration mCross -i sample.crosslinks.bed -g genome.fa -k 7 -n 5 -o mcross_out Step 3: Intersect with heterozygous SNPs for allele-specific binding bedtools intersect -wa -wb -s -a sample.crosslinks.bed -b het_snps.vcf > cl_at_hets.bed Step 4: Test allele bias with BEAPR or ASPRIN
What does the bio-clip-seq-crosslink-site-detection skill do?
Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill crosslink-site-detection --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.