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NeVibeCode · 676 items

Skills for Science and research

Skills for Science and research: what each one does, an install command and example prompts.

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 +1 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 +1 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 +1 1,900installs pyhealth K-Dense-AI skill Builds and validates PyHealth pipelines for clinical data: EHR, signals, imaging, medical codes. Useful when modelling mortality, readmission or length of stay. CX Codex +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 1,900installs deeptools K-Dense-AI skill A skill that turns sequencing data into coverage tracks, QC metrics and heatmaps around TSS and peaks. CX Codex +1 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 +1 1,900installs astropy K-Dense-AI skill Helps an agent write and debug Astropy code for astronomy data. Use it for coordinate transforms, FITS files, tables, and time calculations. CX Codex +1 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 +1 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 +1 1,900installs clinical-decision-support K-Dense-AI skill Builds and checks research-only clinical decision-support artifacts: evidence profiles, cohorts, survival plans, de-identification. Not for patient care. CX Codex +1 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 +1 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 +1 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 +1 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 +1 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 +1 1,900installs what-if-oracle K-Dense-AI skill Walks a research plan through what-if branches: favorable, reference, adverse and more. Shows where the plan breaks before you spend resources on it. CX Codex +1 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 +1 1,900installs geomaster K-Dense-AI skill Guides geospatial research work with satellite imagery, vector and raster GIS data, coordinate systems, spatial statistics, and Earth observation models. CX Codex +1 1,900installs pymoo K-Dense-AI skill A skill that drives pymoo from your agent: algorithm choice, problem setup, constraints and Pareto front analysis. Useful when objectives conflict. CX Codex +1 1,900installs scikit-bio K-Dense-AI skill Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. Helpful for microbiome workflows and ecology data. CX Codex +1 1,900installs geopandas K-Dense-AI skill Guides Python geospatial workflows using GeoPandas, audits vector geometries, and verifies CRS transformations before execution. CX Codex +1 1,900installs research-lookup K-Dense-AI skill Collects verified academic articles and references for a manuscript or review when you need 60+ sources. Uses parallel search, extracts data from PDFs and web sources, supports deep exhaustive search and optional Perplexity. CX Codex +1 1,900installs biopython K-Dense-AI skill Automates computational biology workflows: parses sequence files, runs alignments, and fetches records via NCBI Entrez. CX Codex +1 2,000installs torch-geometric K-Dense-AI skill Guides work with PyTorch Geometric graph neural networks, from graph data setup to classification tasks. Use it when a project relies on torch_geometric. CX Codex +1 2,000installs venue-templates K-Dense-AI skill Prepares journal manuscripts, conference papers, research posters, and grant documents with current venue rules and bundled LaTeX scaffolds. Verifies page limits, anonymity requirements, and formatting before submission. CX Codex +1 2,000installs open-notebook K-Dense-AI skill Organizes research notes, citations, and document chat using self-hosted storage and AI providers. Helpful for managing an Open Notebook setup directly from your agent. CX Codex +1 2,000installs sr-screener Imbad0202 skill Applies protocol-driven screening to study records for reviews. It manages double-blind screening of titles, abstracts, and full texts. CX Codex +1 469installs

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