AI prompts and agent skills.

By K-Dense-AIOriginal project

MIT · FreeView skill

SkillData & Analytics

Bulk RNA-seq

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathwa...

✳Claude Code>_Codex◈OpenClaw+1

By K-Dense-AIOriginal project

MIT · FreeView skill

SkillData & Analytics

🧪 UKB-PPP Region Fetch

Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement. Use when an agent needs per-variant beta / SE / p-value around a coloc-lead variant for downstream colocalisation, Mend...

◈OpenClaw

By ClawBioOriginal project

MIT · FreeView skill

SkillData & Analytics

Divergence Time Estimation -- A Date Is Mostly the Calibration Prior, Not the Sequence

Estimate divergence times under molecular-clock models with BEAST2, MCMCTree/PAML, TreePL, and LSD2, framing a date as a product of the calibration prior and the clock model far more than of the sequence data. Covers why branch length = rate x time is nonidentifiable so only calibrations convert ...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Treatment Effect Measures for Clinical Trials

Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting t...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Power and Sample Size for Clinical Trials

Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 8...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

methylKit Analysis

Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results spine - filterByCoverage, normalizeCoverage, unite/destrand, calculateDiffMeth, getMethylDiff - for both per-CpG (DMC) and fixed-tile (DMR) differential methylation, plus tileMethylC...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

QSAR Modeling

Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, cal...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

TCM Biomedical Research Strategist

Designs complete, rigorous research plans for medicinal plant / TCM molecular mechanism studies against diseases (colorectal cancer, liver cancer, diabetes, etc.). Use whenever a user provides a broad herbal medicine or network pharmacology research direction and wants it translated into a struct...

✳Claude Code>_Codex◈OpenClaw+1

By GeorgeDoors888Original project

3 GitHub stars

MIT · FreeView skill

SkillData & Analytics

edgeR Basics

Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

COPYRIGHT NOTICE

Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Survival Analysis Guide

Conduct Kaplan-Meier, Cox regression, and time-to-event analyses

◈OpenClaw

By wentoraiOriginal project

307 GitHub stars

MIT · FreeView skill

SkillData & Analytics

Single-Cell RNA-seq Pipeline

Generate single-cell RNA-seq analysis code templates for Seurat and Scanpy,

◈OpenClaw

By GeorgeDoors888Original project

3 GitHub stars

MIT · FreeView skill

SkillData & Analytics

Adapter Trimming

Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

CDISC SDTM and ADaM Data Handling

Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and...

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By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Deep Learning for ChIP-seq

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Chromatin State Segmentation

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Elastic Net Feature Selection

Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path and cross-validation plots. Trigger keywords: elastic net, glmnet, feature selection, binary cla...

◈OpenClaw

By aibot88Original project

6 GitHub stars

MIT · FreeView skill

SkillData & Analytics

Protein Structure Data Retrieval

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures...

◈OpenClaw

Business Intelligence Analyst Academic Writer

By FreedomIntelligenceOriginal project

MIT · FreeView skill

SkillData & Analytics

Europe PMC API Guide

Search biomedical and life sciences literature via Europe PMC

◈OpenClaw

By wentoraiOriginal project

307 GitHub stars

MIT · FreeView skill

SkillData & Analytics

Metabolomics Research

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties...

✳Claude Code>_Codex◈OpenClaw+1