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Skill

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backend-dev-guidelines sickn33/ic-awesome-skills/backend-dev-guidelines You are a senior backend engineer operating production-grade services under strict architectural and reliability cons…

sickn33/ic-awesome-skills

arboreto k-dense-ai/scientific--skills/arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).

k-dense-ai/scientific--skills

adaptyv k-dense-ai/scientific--skills/adaptyv How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieva…

k-dense-ai/scientific--skills

fluidsim k-dense-ai/scientific--skills/fluidsim Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explici…

k-dense-ai/scientific--skills

molecular-dynamics k-dense-ai/scientific--skills/molecular-dynamics Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis.

k-dense-ai/scientific--skills

pydeseq2 k-dense-ai/scientific--skills/pydeseq2 Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR co…

k-dense-ai/scientific--skills

contribute-skill fandhe-ai/-cli-skills/contribute-skill ローカルで改修した `skills/<skill-name>/` を upstream リポジトリ (Fandhe-AI/-cli-skills 等) へ PR として投稿する…

fandhe-ai/-cli-skills

imaging-data-commons k-dense-ai/scientific--skills/imaging-data-commons Query and download public cancer imaging data from NCI Imaging Data Commons.

k-dense-ai/scientific--skills

torchdrug k-dense-ai/scientific--skills/torchdrug Build and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraini…

k-dense-ai/scientific--skills

pymatgen k-dense-ai/scientific--skills/pymatgen Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs…

k-dense-ai/scientific--skills

pyhealth k-dense-ai/scientific--skills/pyhealth Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, …

k-dense-ai/scientific--skills

esm k-dense-ai/scientific--skills/esm Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFo…

k-dense-ai/scientific--skills

zarr-python k-dense-ai/scientific--skills/zarr-python Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/…

k-dense-ai/scientific--skills

neurokit2 k-dense-ai/scientific--skills/neurokit2 Use NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing, event/in…

k-dense-ai/scientific--skills

scvi-tools k-dense-ai/scientific--skills/scvi-tools Deep generative models for single-cell omics.

k-dense-ai/scientific--skills

dhdna-profiler k-dense-ai/scientific--skills/dhdna-profiler Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how…

k-dense-ai/scientific--skills

ui-design starchild-ai-/official-skills/ui-design UI/UX quality gate and build guide for every visual output — landing pages, dashboards, web apps, portfolios, and too…

starchild-ai-/official-skills

cirq k-dense-ai/scientific--skills/cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…

k-dense-ai/scientific--skills

diffdock k-dense-ai/scientific--skills/diffdock DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus S…

k-dense-ai/scientific--skills

pysam k-dense-ai/scientific--skills/pysam Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, F…

k-dense-ai/scientific--skills

cobrapy k-dense-ai/scientific--skills/cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…

k-dense-ai/scientific--skills

depmap k-dense-ai/scientific--skills/depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivi…

k-dense-ai/scientific--skills

medchem k-dense-ai/scientific--skills/medchem Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert c…

k-dense-ai/scientific--skills

pathml k-dense-ai/scientific--skills/pathml Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and …

k-dense-ai/scientific--skills

molfeat k-dense-ai/scientific--skills/molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…

k-dense-ai/scientific--skills

treatment-plans k-dense-ai/scientific--skills/treatment-plans Format and structurally validate local treatment-plan documentation after clinical decisions have already been suppli…

k-dense-ai/scientific--skills

geniml k-dense-ai/scientific--skills/geniml Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEm…

k-dense-ai/scientific--skills

labarchive-integration k-dense-ai/scientific--skills/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--skills

pennylane k-dense-ai/scientific--skills/pennylane Hardware-agnostic quantum ML framework with automatic differentiation.

k-dense-ai/scientific--skills

etetoolkit k-dense-ai/scientific--skills/etetoolkit Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4.

k-dense-ai/scientific--skills

flowio k-dense-ai/scientific--skills/flowio Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO.

k-dense-ai/scientific--skills

pytdc k-dense-ai/scientific--skills/pytdc Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-…

k-dense-ai/scientific--skills

video-analysis starchild-ai-/official-skills/video-analysis Video understanding for any model \u2014 native passthrough for small\ \ files,\nframe extraction + audio transcripti…

starchild-ai-/official-skills

phylogenetics k-dense-ai/scientific--skills/phylogenetics Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (…

k-dense-ai/scientific--skills

scvelo k-dense-ai/scientific--skills/scvelo RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajec…

k-dense-ai/scientific--skills

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

k-dense-ai/scientific--skills

usfiscaldata k-dense-ai/scientific--skills/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--skills

matchms k-dense-ai/scientific--skills/matchms Process, clean, compare, and search tandem mass spectra with matchms.

k-dense-ai/scientific--skills

gtars k-dense-ai/scientific--skills/gtars Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenizatio…

k-dense-ai/scientific--skills

histolab k-dense-ai/scientific--skills/histolab Lightweight WSI tile extraction and preprocessing.

k-dense-ai/scientific--skills

lamindb k-dense-ai/scientific--skills/lamindb Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.

k-dense-ai/scientific--skills

n8n-self-hosting czlonkowski/n8n-skills/n8n-self-hosting Deploy a production self-hosted n8n end-to-end to a fresh Linux VM over SSH, using Docker Compose behind a Caddy reve…

czlonkowski/n8n-skills

qiskit k-dense-ai/scientific--skills/qiskit Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime.

k-dense-ai/scientific--skills

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

k-dense-ai/scientific--skills

xlsx k-dense-ai/scientific--skills/xlsx Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary del…

k-dense-ai/scientific--skills

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

k-dense-ai/scientific--skills

pyopenms k-dense-ai/scientific--skills/pyopenms Complete mass spectrometry analysis platform.

k-dense-ai/scientific--skills

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

k-dense-ai/scientific--skills

latchbio-integration k-dense-ai/scientific--skills/latchbio-integration Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Regis…

k-dense-ai/scientific--skills

steel-session-debugging steel-dev/skills/steel-session-debugging Use this skill when the user provides a failed Steel session ID, failed automation run, timeout, error, block…

steel-dev/skills