K-Dense-AI/scientific-agent-skills agent skills, page 3

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX.

K-Dense-AI/scientific-agent-skills

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows.

K-Dense-AI/scientific-agent-skills

GPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster.

K-Dense-AI/scientific-agent-skills

Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK.

K-Dense-AI/scientific-agent-skills

Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows.

K-Dense-AI/scientific-agent-skills

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference.

K-Dense-AI/scientific-agent-skills

Builds with and operates Pi, the minimal terminal coding harness.

K-Dense-AI/scientific-agent-skills

Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.

K-Dense-AI/scientific-agent-skills

Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review.

K-Dense-AI/scientific-agent-skills

Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data.

K-Dense-AI/scientific-agent-skills

Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ…

K-Dense-AI/scientific-agent-skills

Processes mass spectrometry data with pyOpenMS. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance.

K-Dense-AI/scientific-agent-skills

Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing.

K-Dense-AI/scientific-agent-skills

Supports machine learning in Python with scikit-learn. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Builds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and…

K-Dense-AI/scientific-agent-skills

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression.

K-Dense-AI/scientific-agent-skills

Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C), Gymnasium custom environments, vectorized rollouts, callbacks, and checkpoint…

K-Dense-AI/scientific-agent-skills

Calculates sample sizes and statistical power for study planning.

K-Dense-AI/scientific-agent-skills

Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation.

K-Dense-AI/scientific-agent-skills

Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required.

K-Dense-AI/scientific-agent-skills

Stores and retrieves genomic variant calls with TileDB-VCF. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Performs zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile forecasts, XReg covariates, and held-out evaluation.

K-Dense-AI/scientific-agent-skills

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and…

K-Dense-AI/scientific-agent-skills

Queries the U.S. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion.

K-Dense-AI/scientific-agent-skills

Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task…

K-Dense-AI/scientific-agent-skills

Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions.

K-Dense-AI/scientific-agent-skills

Stores and queries chunked N-D scientific arrays with Zarr-Python 3, including codecs, sharding, S3/GCS storage, and NumPy/Dask/Xarray integration.

K-Dense-AI/scientific-agent-skills

Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement.

K-Dense-AI/scientific-agent-skills

Deep learning framework (PyTorch Lightning / lightning package).

K-Dense-AI/scientific-agent-skills

Builds slide decks and presentations for research talks. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance.

K-Dense-AI/scientific-agent-skills

Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights.

K-Dense-AI/scientific-agent-skills

Queries and downloads public cancer imaging data from NCI Imaging Data Commons.

K-Dense-AI/scientific-agent-skills

Supports PyTorch Geometric (PyG) graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets.

K-Dense-AI/scientific-agent-skills

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).

K-Dense-AI/scientific-agent-skills

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results.

K-Dense-AI/scientific-agent-skills

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

K-Dense-AI/scientific-agent-skills

Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for…

K-Dense-AI/scientific-agent-skills

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

K-Dense-AI/scientific-agent-skills

Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text.

K-Dense-AI/scientific-agent-skills

Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple…

K-Dense-AI/scientific-agent-skills

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis.

K-Dense-AI/scientific-agent-skills

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI.

K-Dense-AI/scientific-agent-skills

High-performance DataFrame library for Python ETL, analytics, and pandas migration.

K-Dense-AI/scientific-agent-skills