Skills for Claude Code, Codex and Cursor

matchms K-Dense-AI Cleans, filters, and compares tandem mass spectra using matchms. Useful for searching MS/MS reference libraries, calculating spectral similarity, and building score matrices. Claude Code CX Codex Cursor +1 1,900installs usfiscaldata K-Dense-AI Queries U.S. Treasury fiscal data for debt, statements, rates and auctions through a REST API. Use it when federal financial figures are needed without an API key. Claude Code CX Codex Cursor +1 1,900installs scvelo K-Dense-AI Runs RNA velocity analysis from spliced and unspliced count matrices using scVelo. Useful for directional trajectory hypotheses alongside Scanpy workflows. Claude Code CX Codex Cursor +1 1,900installs phylogenetics K-Dense-AI Skill for aligning DNA and protein sequences, inferring phylogenetic trees with branch support calculation, and visualizing results. For researchers in bioinformatics, microbiology, and molecular evolution. Claude Code CX Codex Cursor +1 1,900installs pytdc K-Dense-AI Integrates Therapeutics Data Commons workflows into coding agents to discover ML datasets, plan task splits, and run molecular oracles safely. Claude Code CX Codex Cursor +1 1,900installs geniml K-Dense-AI Checks BED and genomic-universe contracts, then plans Region2Vec and scEmbed runs. Use it before local genomic-interval analysis. Claude Code CX Codex Cursor +1 1,900installs etetoolkit K-Dense-AI Analyzes phylogenetic trees with the ETE 4 library: compares topologies, annotates nodes, detects gene duplications, queries NCBI and GTDB taxonomy, and renders publication figures. Claude Code CX Codex Cursor +1 1,900installs pennylane K-Dense-AI Guides an agent in setting up PennyLane 0.45.1 quantum circuits, variational VQE algorithms, and hybrid neural models. Claude Code CX Codex Cursor +1 1,900installs labarchive-integration K-Dense-AI This skill guides work with LabArchives ELN API and Inventory API v1, including regional endpoints, request signing, and local request planning. Claude Code CX Codex Cursor +1 1,900installs molfeat K-Dense-AI Converts molecular structures into fingerprints, descriptors, and embeddings for machine learning, similarity search, and screening. Requires Python 3.11+, RDKit, and PyTorch. Claude Code CX Codex Cursor +1 1,900installs pathml K-Dense-AI Guides computational pathology workflows using PathML 3.0.8. It handles whole-slide image tiling, tissue detection, and .h5path exports locally. Claude Code CX Codex Cursor +1 1,900installs cobrapy K-Dense-AI Guides COBRApy-based metabolic model analysis, from flux calculations and gene knockouts to media design and SBML checks. Claude Code CX Codex Cursor +1 1,900installs depmap K-Dense-AI A skill for discovering and analyzing Cancer Dependency Map data. Helps examine CRISPR Chronos gene effects, co-essentiality, and PRISM compound responses. Claude Code CX Codex Cursor +1 1,900installs diffdock K-Dense-AI Docks a small molecule into a protein with DiffDock and DiffDock-L, for one pair or a batch, then hands back ranked candidate poses. Claude Code CX Codex Cursor +1 1,900installs pysam K-Dense-AI Guides agents through Python and HTSlib workflows for genomic files like BAM, CRAM, and VCF. Useful when extracting alignments, filtering reads, and computing coverage. Claude Code CX Codex Cursor +1 1,900installs medchem K-Dense-AI Filters compound libraries with drug-likeness rules, structural alerts, and complexity checks. Use it when triaging molecular candidates. Claude Code CX Codex Cursor +1 1,900installs dhdna-profiler K-Dense-AI A skill that applies the DHDNA framework to describe reasoning and writing patterns in text. Use it when you need reflection on thinking style, a cognitive-preference profile, or comparison of how texts construct arguments. Claude Code CX Codex Cursor +1 1,900installs neurokit2 K-Dense-AI Builds reproducible physiological time-series workflows in NeuroKit2 0.2.13. Helps audit biosignals, verify data contracts, and prevent package conflicts. Claude Code CX Codex Cursor +1 1,900installs scvi-tools K-Dense-AI Guides probabilistic modelling for single-cell omics data. Use it for batch integration, cell annotation, multimodal data, and model-based uncertainty. Claude Code CX Codex Cursor +1 1,900installs paperzilla K-Dense-AI A skill that lets your agent access Paperzilla projects, recommendations, and papers through the CLI. Use it to find relevant work, browse project feeds, search recommendations, and export results. Claude Code CX Codex Cursor +1 1,900installs zarr-python K-Dense-AI Stores and queries chunked N-D scientific arrays with Zarr-Python 3. Useful for configuring sharding, codecs, and remote storage access. Claude Code CX Codex Cursor +1 1,900installs esm K-Dense-AI A skill for Biohub's esm Python SDK: ESM3 protein generation, ESMC embeddings and ESMFold2 all-atom folding, run locally or through a hosted client. Claude Code CX Codex Cursor +1 1,900installs torchdrug K-Dense-AI Helps build and debug TorchDrug 0.2.1 pipelines for molecular graphs and proteins. Use it when training property prediction, molecule generation, or retrosynthesis models. Claude Code CX Codex Cursor +1 1,900installs pymatgen K-Dense-AI Analyzes, validates, converts, and transforms materials structures and computed data with pymatgen. Use it for phase diagrams, symmetry checks, electronic-structure files, and bounded Materials Project queries. Claude Code CX Codex Cursor +1 1,900installs imaging-data-commons K-Dense-AI Skill for searching and downloading public medical imaging data from the NCI Imaging Data Commons repository. Works with DICOM, CT, MR, PET and digital pathology without authentication for basic queries. Claude Code CX Codex Cursor +1 1,900installs fluidsim K-Dense-AI Sets up, validates, and analyzes bounded FluidSim CFD simulations with strict resource limits and HPC safety checks. Claude Code CX Codex Cursor +1 1,900installs molecular-dynamics K-Dense-AI Runs molecular dynamics in OpenMM and analyses the trajectories with MDAnalysis: RMSD, RMSF, contact maps, free energy surfaces. Claude Code CX Codex Cursor +1 1,900installs pydeseq2 K-Dense-AI Skill for differential expression analysis of RNA-seq count data. Performs negative-binomial GLM with explicit biological replicates, design formulas, and statistical contrasts. Claude Code CX Codex Cursor +1 1,900installs adaptyv K-Dense-AI Helps design protein characterization assays in Adaptyv Bio Foundry, check catalog targets, estimate run budgets, and collect test results. Claude Code CX Codex Cursor +1 1,900installs arboreto K-Dense-AI Ranks candidate regulator-target pairs from expression data: GRNBoost2 with gradient boosting, GENIE3 with random forests. Needs a gene table and a TF list. Claude Code CX Codex Cursor +1 1,900installs vaex K-Dense-AI A skill for columnar analysis on a single machine when data exceeds available memory. Process HDF5, Arrow, CSV, and Parquet through lazy Vaex expressions, virtual columns, and streamed statistics. Claude Code CX Codex Cursor +1 1,900installs benchling-integration K-Dense-AI Automates Benchling laboratory data workflows using Python SDK 1.25.0 and REST API v2. Useful for managing registry entities, sample inventory, and ELN entries. Claude Code CX Codex Cursor +1 1,900installs datamol K-Dense-AI Guides an agent through molecular data work with datamol and RDKit, from SMILES parsing to descriptors, clustering, and 3D conformers. Claude Code CX Codex Cursor +1 1,900installs cellxgene-census K-Dense-AI A skill for programmatic access to CZ CELLxGENE Census, a vast catalog of standardized single-cell transcriptomics data. Query metadata, gene expression, and embeddings without downloading entire datasets. Claude Code CX Codex Cursor +1 1,900installs deepchem K-Dense-AI Builds molecular property prediction and MoleculeNet pipelines in DeepChem 2.8.0. Useful for SMILES featurization and scaffold-based ML. Claude Code CX Codex Cursor +1 1,900installs pufferlib K-Dense-AI Skill for PufferLib: choose between native 5.0, PyPI 3.0.0, or pinned 4.0, validate Gymnasium contracts, adapt environments, and review checkpoints safely. Requires Python 3.10+ and native C/CUDA for training. Claude Code CX Codex Cursor +1 1,900installs pydicom K-Dense-AI Inspects and processes local DICOM files, transfer syntaxes, and pixel data. Enforces strict metadata allowlists to prevent sensitive patient data from leaking into logs. Claude Code CX Codex Cursor +1 1,900installs scanpy K-Dense-AI A skill with ready-made CLI scripts for the full single-cell RNA-seq workflow: QC, normalization, clustering, marker genes, visualization. Use it when you want Scanpy results without writing the pipeline by hand. Claude Code CX Codex Cursor +1 1,900installs rdkit K-Dense-AI Guides coding agents through cheminformatics tasks in Python, including SMILES parsing, descriptor calculations, and 3D coordinate generation. Claude Code CX Codex Cursor +1 1,900installs modal K-Dense-AI Guides Python workloads on Modal, from web endpoints to GPU model training. Use it when deploying cloud jobs through the Modal SDK. Claude Code CX Codex Cursor +1 1,900installs