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k-dense-ai/scientific-agent-skills

214 skills · 210.2K combined installs

Skills from this source

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Skill

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8W Activity

Installs

venue-templates Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting…

k-dense-ai/scientific-agent-skills

biopython Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogeneti…

k-dense-ai/scientific-agent-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-agent-skills

anndata Data structure for annotated matrices in single-cell analysis.

k-dense-ai/scientific-agent-skills

arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).

k-dense-ai/scientific-agent-skills

astropy Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coor…

k-dense-ai/scientific-agent-skills

benchling-integration Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling App…

k-dense-ai/scientific-agent-skills

bioservices Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL,…

k-dense-ai/scientific-agent-skills

cellxgene-census Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.

k-dense-ai/scientific-agent-skills

clinical-decision-support Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarke…

k-dense-ai/scientific-agent-skills

clinical-reports Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safet…

k-dense-ai/scientific-agent-skills

consciousness-council Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill wh…

k-dense-ai/scientific-agent-skills

datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults.

k-dense-ai/scientific-agent-skills

deepchem Molecular ML with diverse featurizers and pre-built datasets.

k-dense-ai/scientific-agent-skills

deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …

k-dense-ai/scientific-agent-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-agent-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-agent-skills

fluidsim Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explici…

k-dense-ai/scientific-agent-skills

geomaster Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth obs…

k-dense-ai/scientific-agent-skills

geopandas Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial oper…

k-dense-ai/scientific-agent-skills

gget Fast CLI/Python queries to 20+ bioinformatics databases.

k-dense-ai/scientific-agent-skills

hypogenic Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text data…

k-dense-ai/scientific-agent-skills

imaging-data-commons Query and download public cancer imaging data from NCI Imaging Data Commons.

k-dense-ai/scientific-agent-skills

modal Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or se…

k-dense-ai/scientific-agent-skills

molecular-dynamics Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis.

k-dense-ai/scientific-agent-skills

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

k-dense-ai/scientific-agent-skills

pathml Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and …

k-dense-ai/scientific-agent-skills

pufferlib Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, …

k-dense-ai/scientific-agent-skills

pydeseq2 Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR co…

k-dense-ai/scientific-agent-skills

pydicom Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to …

k-dense-ai/scientific-agent-skills

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

k-dense-ai/scientific-agent-skills

pymatgen Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs…

k-dense-ai/scientific-agent-skills

pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZD…

k-dense-ai/scientific-agent-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-agent-skills

rdkit Cheminformatics toolkit for fine-grained molecular control.

k-dense-ai/scientific-agent-skills

research-lookup Compile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks t…

k-dense-ai/scientific-agent-skills

scanpy Standard single-cell RNA-seq analysis pipeline.

k-dense-ai/scientific-agent-skills

scikit-bio Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), …

k-dense-ai/scientific-agent-skills

scvi-tools Deep generative models for single-cell omics.

k-dense-ai/scientific-agent-skills

simpy Build, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, reso…

k-dense-ai/scientific-agent-skills

stable-baselines3 Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API.

k-dense-ai/scientific-agent-skills

timesfm-forecasting Zero-shot time series forecasting with Google's TimesFM foundation model.

k-dense-ai/scientific-agent-skills

torchdrug Build and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraini…

k-dense-ai/scientific-agent-skills

vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM.

k-dense-ai/scientific-agent-skills

what-if-oracle Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, con…

k-dense-ai/scientific-agent-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-agent-skills

depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivi…

k-dense-ai/scientific-agent-skills

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

k-dense-ai/scientific-agent-skills

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

k-dense-ai/scientific-agent-skills

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

k-dense-ai/scientific-agent-skills