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setup
Set up a new autoresearch experiment with all required configuration. /ar:setup # Interactive mode /ar:setup engine...
nextflow-development
Run nf-core bioinformatics pipelines on local or public sequencing data. Target users: Bench scientists and researchers without specialized bioinforma...
tiledbvcf
TileDB-VCF is a high-performance C++ library with Python and CLI interfaces for efficient storage and retrieval of genomic variant-call data. Built on...
skill-from-notebook
Extract actionable methodologies from learning materials (documents, articles, videos) or quality examples (blog posts, designs, code) to generate reu...
biomcp-server
Deploy and operate the BioMCP server so MCP-compatible clients (Claude Desktop, LobeChat, etc.) can query biomedical databases via a single standardiz...
diffdock
DiffDock is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of small molecule ligands to protein targets. It...
find-skills
This skill helps you discover and install skills from the open agent skills ecosystem. Use this skill when the user: Asks "how do I do X" where X migh...
bio-epidemiological-genomics-amr-surveillance
Reference examples tested with: AMRFinderPlus 3.12+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Pyth...
bio-genome-assembly-scaffolding
bwa index draftassembly.fa bwa mem -5SP -t 16 draftassembly.fa hicR1.fq.gz hicR2.fq.gz | \ samtools view -@ 8 -bhS - > aligned.bam pairtools parse --m...
bio-imaging-mass-cytometry-data-preprocessing
Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, steinbock 0.16+ Before using code patterns, verify...
open-notebook
Open Notebook is an open-source, self-hosted alternative to Google's NotebookLM that enables researchers to organize materials, generate AI-powered in...
bio-workflow-management-snakemake-workflows
Compatible with Snakemake 7.x, 8.x, and 9.x. For Snakemake 8.0+, use --executor instead of --cluster. rule all: input: expand("results/{sample}counts....