bio-clip-seq-binding-site-annotation
Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.
npx skills add BioTender-max/awesome-bio-agent-skills --skill binding-site-annotation --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: ChIPseeker 1.40+, RCAS 1.30+, GenomicFeatures 1.56+, GenomicRanges 1.56+, rbp-maps (Yeo github), bedtools 2.31+, pybedtools 0.10+, pyranges 0.0.129+. Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws unexpected errors, introspect the installed package and adapt the example to match the actual API rather than retrying. ChIPseeker 1.40+ changed the priority defaults; verify the priority vector before pipelining. # Binding Site Annotation **"Annotate where in transcripts my RBP binds"** -> Map CLIP peaks or single-nucleotide crosslink sites to RNA features and report the per-feature distribution. The interpretation is RBP-class-specific: splicing factors (PTBP1, U2AF2, RBFOX) bind intron-exon junctions; mRNA-stability regulators (HuR, PUM2) bind 3' UTRs; translation factors (EIF3J, RPS19) bind 5' UTRs and CDS; and small-ncRNA-binding RBPs (NSUN2 tRNAs, LARP7 7SK, TROVE2
- Version Compatibility
- Algorithmic Taxonomy
- Critical Choice: Annotation Hierarchy
- RBP Class -> Expected Annotation
- RBP-Maps: Splicing Regulatory Maps
- Per-Tool Failure Modes
- ChIPseeker -- TSS-region default over-extends
- ChIPseeker -- Gene-level loses isoform context
- RCAS -- Slow on large peak sets
- RBP-Maps -- Requires SE event table
- bedtools -- Manual hierarchy errors
- Repeat-element overlap missed
- Mitochondrial peaks excluded by default
- Strand information ignored
Yeo lab rbp-maps Snakemake workflow git clone https://github.com/YeoLab/rbp-maps cd rbp-maps python rbpmaps/RBPMaps.py \ deepTools computeMatrix for metagene Step 1: peaks BED -> bedgraph bedtools genomecov -bg -strand + -ibam dedup.bam > clip_plus.bg bedtools genomecov -bg -strand - -ibam dedup.bam > clip_minus.bg combine to bigwig bedGraphToBigWig clip_plus.bg chrom.sizes clip_plus.bw
What does the bio-clip-seq-binding-site-annotation skill do?
Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill binding-site-annotation --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.