AI prompts and agent skills.

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

OMERO Integration

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

◈OpenClaw

By DicklesworthstoneOriginal project

1,947 GitHub stars

MIT · FreeView skill

SkillData & Analytics

PyTDC (Therapeutics Data Commons)

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

◈OpenClaw

By DicklesworthstoneOriginal project

1,947 GitHub stars

MIT · FreeView skill

SkillData & Analytics

gsea

Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Pseudotime Trajectory Visualization

Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Sequence Alignment

A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Survival Analysis (Kaplan-Meier)

Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.

◈OpenClaw

By aipochOriginal project

Business Intelligence Analyst Data Analyst

MIT · FreeView skill

SkillData & Analytics

Open Source License Check

Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Target Novelty Scorer

Score the novelty of biological targets through literature mining and.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Circos Plot Generator

Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Table 1 Generator

Automated generation of baseline characteristics tables (Table 1) for clinical research papers.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Methylation Calling

Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismark_methylation_extractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the beta value M/(M+U) as a coverage file, bedGraph, or genome-wide cytosine report across CpG/CHG/CH...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

bedGraph Handling

Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across sample...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

DNAnexus Integration

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Proximity Operations

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Coverage Analysis

Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-con...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Chromatin Loop Calling

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Epitope Prediction

Predict B-cell and T-cell epitopes for vaccine antigen design and epitope mapping with BepiPred-3.0, DiscoTope-3.0, the IEDB tools, and EL-mode MHC presentation. Encodes the load-bearing asymmetry that T-cell epitope prediction is mature (it reduces to MHC presentation, AUC>0.9) while B-cell pred...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Lipidomics Analysis

Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware differential and enrichment analysis with lipidr, guarding against in-source-fragment phantoms, sn-position over-claims, and invalid cross-class quantification. Use when naming or ca...

↗Cursor

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

XCMS Untargeted LC-MS Preprocessing

Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature f...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Metabolomics Pathway Mapping

Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with correct background-set construction and honest interpretive ceilings. Use when interpreting differe...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Abundance Estimation

Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositional treatment (CLR, zero handling), library-size normalization, reference-frame differential abundance, and optional absolute quantification. Covers why a relative-abundance chang...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Functional Prediction with PICRUSt2

Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic interpolation of reference-genome gene content - EPA-ng placement, gappa, castor hidden-state prediction of KO/EC/Pfam copy number, 16S copy-number normalization, and MinPath MetaCyc/...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project