bio-small-rna-seq-target-prediction
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.
npx skills add majiayu000/claude-skill-registry --skill target-prediction-gptomics-bioskills --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.
# miRNA Target Prediction ## miRanda Algorithm ```bash # Run miRanda for target prediction miranda miRNA.fa UTRs.fa \ -sc 140 \ -en -20 \ -out predictions.txt # Options: # -sc 140: Minimum alignment score (default 140) # -en -20: Maximum free energy threshold (kcal/mol) # Higher score and lower energy = stronger prediction ``` ## Parse miRanda Output ```python import pandas as pd def parse_miranda(output_file): '''Parse miRanda output file''' results = [] with open(output_file) as f: for line in f: if line.startswith('>'): parts = line.strip().split('\t') if len(parts) >= 5: results.append({ 'mirna': parts[0].lstrip('>'), 'target': parts[1], 'score': float(parts[2]), 'energy': float(parts[3]), 'position': parts[4] }) return pd.DataFrame(results) ``` ## TargetScan Database Lookup ```python import requests import pandas as pd def query_targetscan(mirna_family): '''Query TargetScan for predicted targets Note: TargetScan uses miRNA family names (e.g., miR-21-5p) ''' # TargetScan provides downloadable files # For human: https://www.targetscan.org/vert_80/vert_80_data_download/ targetscan_file = 'Predicted_Targets_Context_Scores.txt' df = pd.read_csv(targetscan_file, sep='\t') targets =
- miRanda Algorithm
- Parse miRanda Output
- TargetScan Database Lookup
- miRDB Database Lookup
- Combine Multiple Databases
- Python miRNA Target Prediction
- Seed Match Analysis
- Functional Enrichment of Targets
- Related Skills
Run miRanda for target prediction miranda miRNA.fa UTRs.fa \ Higher score and lower energy = stronger prediction
What does the bio-small-rna-seq-target-prediction skill do?
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill target-prediction-gptomics-bioskills --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 majiayu000/claude-skill-registry, a repository with 534 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.