k-dense-ai/scientific-agent-skills

8635

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

k-dense-ai/scientific-agent-skills

1.8K

8634

treatment-plans Format and structurally validate local treatment-plan documentation after clinical decisions have already been suppli…

k-dense-ai/scientific-agent-skills

1.8K

8642

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

k-dense-ai/scientific-agent-skills

1.8K

8641

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

1.8K

8640

pennylane Hardware-agnostic quantum ML framework with automatic differentiation.

k-dense-ai/scientific-agent-skills

1.8K

8647

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

k-dense-ai/scientific-agent-skills

1.8K

8648

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

1.8K

8653

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

k-dense-ai/scientific-agent-skills

1.8K

8659

phylogenetics Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (…

k-dense-ai/scientific-agent-skills

1.8K

8663

scvelo RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajec…

k-dense-ai/scientific-agent-skills

1.8K

8667

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

1.8K

8668

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

1.8K

8672

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

k-dense-ai/scientific-agent-skills

1.8K

8680

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

k-dense-ai/scientific-agent-skills

1.8K

8678

histolab Lightweight WSI tile extraction and preprocessing.

k-dense-ai/scientific-agent-skills

1.8K

8681

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

k-dense-ai/scientific-agent-skills

1.8K

8679

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

k-dense-ai/scientific-agent-skills

1.8K

8685

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

k-dense-ai/scientific-agent-skills

1.8K

8686

xlsx Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary del…

k-dense-ai/scientific-agent-skills

1.8K

8689

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

k-dense-ai/scientific-agent-skills

1.8K

8690

pyopenms Complete mass spectrometry analysis platform.

k-dense-ai/scientific-agent-skills

1.8K

8694

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

1.8K

8695

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

1.8K

8696

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

k-dense-ai/scientific-agent-skills

1.8K

8701

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

k-dense-ai/scientific-agent-skills

1.8K

8702

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

k-dense-ai/scientific-agent-skills

1.8K

8703

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

1.8K

8708

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

1.8K

8715

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

k-dense-ai/scientific-agent-skills

1.8K

8723

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

k-dense-ai/scientific-agent-skills

1.8K

8729

glycoengineering Analyze and engineer protein glycosylation.

k-dense-ai/scientific-agent-skills

1.8K

8732

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

k-dense-ai/scientific-agent-skills

1.8K

8736

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

1.8K

9072

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

1.6K

9178

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

k-dense-ai/scientific-agent-skills

1.6K

9329

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

1.6K

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