Claude Code skills, plugins, subagents, slash commands and mcp servers

etetoolkit K-Dense-AI skill Analyzes phylogenetic trees with the ETE 4 library: compares topologies, annotates nodes, detects gene duplications, queries NCBI and GTDB taxonomy, and renders publication figures. CX Codex Cursor GitHub Copilot 1,900installs pennylane K-Dense-AI skill Guides an agent in setting up PennyLane 0.45.1 quantum circuits, variational VQE algorithms, and hybrid neural models. CX Codex Cursor GitHub Copilot 1,900installs labarchive-integration K-Dense-AI skill This skill guides work with LabArchives ELN API and Inventory API v1, including regional endpoints, request signing, and local request planning. CX Codex Cursor GitHub Copilot 1,900installs molfeat K-Dense-AI skill Converts molecular structures into fingerprints, descriptors, and embeddings for machine learning, similarity search, and screening. Requires Python 3.11+, RDKit, and PyTorch. CX Codex Cursor GitHub Copilot 1,900installs pathml K-Dense-AI skill Guides computational pathology workflows using PathML 3.0.8. It handles whole-slide image tiling, tissue detection, and .h5path exports locally. CX Codex Cursor GitHub Copilot 1,900installs cobrapy K-Dense-AI skill Guides COBRApy-based metabolic model analysis, from flux calculations and gene knockouts to media design and SBML checks. CX Codex Cursor GitHub Copilot 1,900installs depmap K-Dense-AI skill A skill for discovering and analyzing Cancer Dependency Map data. Helps examine CRISPR Chronos gene effects, co-essentiality, and PRISM compound responses. CX Codex Cursor GitHub Copilot 1,900installs diffdock K-Dense-AI skill Docks a small molecule into a protein with DiffDock and DiffDock-L, for one pair or a batch, then hands back ranked candidate poses. CX Codex Cursor GitHub Copilot 1,900installs pysam K-Dense-AI skill Guides agents through Python and HTSlib workflows for genomic files like BAM, CRAM, and VCF. Useful when extracting alignments, filtering reads, and computing coverage. CX Codex Cursor GitHub Copilot 1,900installs medchem K-Dense-AI skill Filters compound libraries with drug-likeness rules, structural alerts, and complexity checks. Use it when triaging molecular candidates. CX Codex Cursor GitHub Copilot 1,900installs dhdna-profiler K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs neurokit2 K-Dense-AI skill Builds reproducible physiological time-series workflows in NeuroKit2 0.2.13. Helps audit biosignals, verify data contracts, and prevent package conflicts. CX Codex Cursor GitHub Copilot 1,900installs scvi-tools K-Dense-AI skill Guides probabilistic modelling for single-cell omics data. Use it for batch integration, cell annotation, multimodal data, and model-based uncertainty. CX Codex Cursor GitHub Copilot 1,900installs paperzilla K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs zarr-python K-Dense-AI skill Stores and queries chunked N-D scientific arrays with Zarr-Python 3. Useful for configuring sharding, codecs, and remote storage access. CX Codex Cursor GitHub Copilot 1,900installs esm K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs torchdrug K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs pymatgen K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs imaging-data-commons K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs fluidsim K-Dense-AI skill Sets up, validates, and analyzes bounded FluidSim CFD simulations with strict resource limits and HPC safety checks. CX Codex Cursor GitHub Copilot 1,900installs molecular-dynamics K-Dense-AI skill Runs molecular dynamics in OpenMM and analyses the trajectories with MDAnalysis: RMSD, RMSF, contact maps, free energy surfaces. CX Codex Cursor GitHub Copilot 1,900installs pydeseq2 K-Dense-AI skill Skill for differential expression analysis of RNA-seq count data. Performs negative-binomial GLM with explicit biological replicates, design formulas, and statistical contrasts. CX Codex Cursor GitHub Copilot 1,900installs adaptyv K-Dense-AI skill Helps design protein characterization assays in Adaptyv Bio Foundry, check catalog targets, estimate run budgets, and collect test results. CX Codex Cursor GitHub Copilot 1,900installs arboreto K-Dense-AI skill Ranks candidate regulator-target pairs from expression data: GRNBoost2 with gradient boosting, GENIE3 with random forests. Needs a gene table and a TF list. CX Codex Cursor GitHub Copilot 1,900installs vaex K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs benchling-integration K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs datamol K-Dense-AI skill Guides an agent through molecular data work with datamol and RDKit, from SMILES parsing to descriptors, clustering, and 3D conformers. CX Codex Cursor GitHub Copilot 1,900installs cellxgene-census K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs deepchem K-Dense-AI skill Builds molecular property prediction and MoleculeNet pipelines in DeepChem 2.8.0. Useful for SMILES featurization and scaffold-based ML. CX Codex Cursor GitHub Copilot 1,900installs pufferlib K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs pydicom K-Dense-AI skill Inspects and processes local DICOM files, transfer syntaxes, and pixel data. Enforces strict metadata allowlists to prevent sensitive patient data from leaking into logs. CX Codex Cursor GitHub Copilot 1,900installs scanpy K-Dense-AI skill 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. CX Codex Cursor GitHub Copilot 1,900installs rdkit K-Dense-AI skill Guides coding agents through cheminformatics tasks in Python, including SMILES parsing, descriptor calculations, and 3D coordinate generation. CX Codex Cursor GitHub Copilot 1,900installs modal K-Dense-AI skill Guides Python workloads on Modal, from web endpoints to GPU model training. Use it when deploying cloud jobs through the Modal SDK. CX Codex Cursor GitHub Copilot 1,900installs gget K-Dense-AI skill Bioinformatics skill providing unified access to over 20 genomic databases via CLI and Python. Useful for gene lookups, alignments, and protein structure downloads. CX Codex Cursor GitHub Copilot 1,900installs clinical-reports K-Dense-AI skill Builds draft skeletons for clinical reports and checks them with local scripts. Inputs must be synthetic, de-identified, or aggregate data. CX Codex Cursor GitHub Copilot 1,900installs anndata K-Dense-AI skill Skill to create, read, and transform annotated data matrices in h5ad and Zarr formats. Integrates with the scverse ecosystem for transcriptomics and other metadata-rich data analysis. CX Codex Cursor GitHub Copilot 1,900installs bioservices K-Dense-AI skill Guides Python workflows using BioServices to query biological databases. Useful for mapping protein IDs, extracting KEGG pathways, and resolving chemical identifiers. CX Codex Cursor GitHub Copilot 1,900installs hypogenic K-Dense-AI skill Skill to plan and audit HypoGeniC, a tool that generates candidate textual hypotheses from labeled datasets using LLM. Use it if you work with the hypogenic package, its task configs, or HypoBench datasets. CX Codex Cursor GitHub Copilot 1,900installs simpy K-Dense-AI skill Builds, tests, and inspects process-based discrete-event simulations using SimPy. Helpful for modeling service queues, logistics, and resource contention. CX Codex Cursor GitHub Copilot 1,900installs