k-dense-ai/scientific-agent-skills

8149

diffdock DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus S…

k-dense-ai/scientific-agent-skills

1.3K

8150

medchem Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert c…

k-dense-ai/scientific-agent-skills

1.3K

8156

geniml Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEm…

k-dense-ai/scientific-agent-skills

1.3K

8164

pytdc Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-…

k-dense-ai/scientific-agent-skills

1.3K

8172

flowio Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO.

k-dense-ai/scientific-agent-skills

1.3K

8173

gtars Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenizatio…

k-dense-ai/scientific-agent-skills

1.3K

8174

molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…

k-dense-ai/scientific-agent-skills

1.3K

8171

pyopenms Complete mass spectrometry analysis platform.

k-dense-ai/scientific-agent-skills

1.3K

8177

etetoolkit Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4.

k-dense-ai/scientific-agent-skills

1.3K

8178

histolab Lightweight WSI tile extraction and preprocessing.

k-dense-ai/scientific-agent-skills

1.3K

8180

matchms Process, clean, compare, and search tandem mass spectra with matchms.

k-dense-ai/scientific-agent-skills

1.3K

8179

usfiscaldata Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (…

k-dense-ai/scientific-agent-skills

1.3K

8183

pennylane Hardware-agnostic quantum ML framework with automatic differentiation.

k-dense-ai/scientific-agent-skills

1.3K

8185

protocolsio-integration Read, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing…

k-dense-ai/scientific-agent-skills

1.3K

8184

tiledbvcf Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample …

k-dense-ai/scientific-agent-skills

1.3K

8188

cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…

k-dense-ai/scientific-agent-skills

1.3K

8189

labarchive-integration Securely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint se…

k-dense-ai/scientific-agent-skills

1.3K

8190

opentrons-integration Author, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and …

k-dense-ai/scientific-agent-skills

1.3K

8191

rowan Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa a…

k-dense-ai/scientific-agent-skills

1.3K

8194

cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…

k-dense-ai/scientific-agent-skills

1.3K

8195

qutip Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-st…

k-dense-ai/scientific-agent-skills

1.3K

8212

lamindb Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.

k-dense-ai/scientific-agent-skills

1.3K

8211

neuropixels-analysis Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB d…

k-dense-ai/scientific-agent-skills

1.3K

8210

qiskit Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime.

k-dense-ai/scientific-agent-skills

1.3K

8217

dnanexus-integration Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, …

k-dense-ai/scientific-agent-skills

1.3K

8216

polars-bio High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merg…

k-dense-ai/scientific-agent-skills

1.3K

8218

pylabrobot Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-dev…

k-dense-ai/scientific-agent-skills

1.3K

8225

latchbio-integration Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Regis…

k-dense-ai/scientific-agent-skills

1.3K

8224

primekg Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, disease…

k-dense-ai/scientific-agent-skills

1.3K

8233

omero-integration Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, …

k-dense-ai/scientific-agent-skills

1.3K

8238

glycoengineering Analyze and engineer protein glycosylation.

k-dense-ai/scientific-agent-skills

1.3K

8251

ginkgo-cloud-lab Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab…

k-dense-ai/scientific-agent-skills

1.3K

8256

paperzilla Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for rece…

k-dense-ai/scientific-agent-skills

1.3K

8823

autoskill Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-…

k-dense-ai/scientific-agent-skills

1.2K

8695

hugging-science Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate,…

k-dense-ai/scientific-agent-skills

1.2K

9152

exa-search Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search …

k-dense-ai/scientific-agent-skills

1.1K

37

bids Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical…

k-dense-ai/scientific-agent-skills

977

38

iso-13485-certification Prepare and structurally review ISO 13485 QMS scope, controlled documentation, and local evidence manifests. Use for …

k-dense-ai/scientific-agent-skills

918

39

pacsomatic Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.

k-dense-ai/scientific-agent-skills

911

40

liteparse Local document and PDF parsing that returns spatial text with bounding boxes.

k-dense-ai/scientific-agent-skills

885

41

bulk-rnaseq End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), ali…

k-dense-ai/scientific-agent-skills

844

42

pathway-enrichment Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whene…

k-dense-ai/scientific-agent-skills

842

43

nextflow Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextfl…

k-dense-ai/scientific-agent-skills

838

44

experimental-design Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out tr…

k-dense-ai/scientific-agent-skills

777

45

statistical-power Sample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/sam…

k-dense-ai/scientific-agent-skills

749

46

pi-agent Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/setti…

k-dense-ai/scientific-agent-skills

716

47

arbor Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objecti…

k-dense-ai/scientific-agent-skills

702

48

onekgpd Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual …

k-dense-ai/scientific-agent-skills

568

49

tamarind Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via it…

k-dense-ai/scientific-agent-skills

568

50

analytical-method-validation Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing frame…

k-dense-ai/scientific-agent-skills

419