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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.

latex-posters K-Dense-AI skill Creates research posters with three LaTeX packages, compiles PDF, and checks fonts before print. CX Codex +1 2,000installs bgpt-paper-search K-Dense-AI skill Searches BGPT scientific papers by topic or DOI. Extracts full-text experimental evidence, reported statistics, and source provenance. CX Codex +1 2,000installs pptx-posters K-Dense-AI skill Turns a local JSON manifest into one editable, macro-free .pptx poster slide, then audits it before print. CX Codex +1 2,000installs scholar-evaluation K-Dense-AI skill Provides qualitative, evidence-traceable developmental feedback on research drafts and protocols. Audits assessment rubrics without proxy prestige metrics. CX Codex +1 2,100installs pylabrobot K-Dense-AI skill Builds PyLabRobot protocols, checks deck geometry, and simulates liquid handling without touching real lab instruments. CX Codex +1 1,900installs tiledbvcf K-Dense-AI skill This skill stores genomic variants in TileDB-VCF, ingests VCF/BCF files, and queries data by region or sample. Use it for cohort workflows. CX Codex +1 1,900installs omero-integration K-Dense-AI skill A skill that lets your agent inventory and automate microscopy data on OMERO.server: object traversal, metadata export, import planning. CX Codex +1 1,900installs rowan K-Dense-AI skill Runs cloud molecular modeling, docking, and pKa prediction pipelines via Python API. Fits computational chemistry workflows without local GPU infrastructure. CX Codex +1 1,900installs qutip K-Dense-AI skill This skill guides QuTiP 5 quantum-system simulations and checks physical assumptions, dimensions, and numerical convergence. CX Codex +1 1,900installs opentrons-integration K-Dense-AI skill Skill for writing, reviewing, and simulating Opentrons Protocol API v2 protocols in Python. Works with Flex and OT-2 liquid handlers to configure decks, pipettes, modules, and runtime parameters. CX Codex +1 1,900installs dnanexus-integration K-Dense-AI skill Automates genomics workloads on DNAnexus using dx CLI, dxpy, and dxCompiler. Handy when building dxapp.json applets or importing Nextflow and WDL pipelines. CX Codex +1 1,900installs latchbio-integration K-Dense-AI skill A skill that walks the agent through Latch work: Python SDK workflows, Nextflow and Snakemake packaging, image registration, run monitoring. CX Codex +1 1,900installs neuropixels-analysis K-Dense-AI skill Runs the full Neuropixels workflow on SpikeInterface, from raw files to curated units: loading, preprocessing, drift correction, spike sorting, quality metrics. CX Codex +1 1,900installs pyopenms K-Dense-AI skill Processes mass spectrometry data for proteomics and metabolomics using pyOpenMS. It detects features, identifies peptides, and generates multi-sample quantification matrices. CX Codex +1 1,900installs polars-bio K-Dense-AI skill Genomic interval arithmetic on Polars DataFrames, plus readers and writers for formats from BED to CRAM. Built for coordinate-aware joins in a Python pipeline. CX Codex +1 1,900installs gtars K-Dense-AI skill Skill for genomic interval analysis, overlaps, consensus and coverage via Python, Rust and CLI. Requires Python 3.10+ and gtars 0.10.0; local tools run offline. CX Codex +1 1,900installs histolab K-Dense-AI skill Prepares whole-slide histology images by segmenting tissue masks, extracting tiles, and normalizing H&E staining. CX Codex +1 1,900installs qiskit K-Dense-AI skill Skill for quantum algorithm development: builds circuits, transpiles them for specific hardware, runs on simulators or IBM quantum processors. Requires Python 3.10+ and optional components depending on your use case. CX Codex +1 1,900installs lamindb K-Dense-AI skill Keeps a LaminDB registry of biological datasets and models: artifact registration, schemas, Bionty annotation, metadata search. CX Codex +1 1,900installs matchms K-Dense-AI skill Cleans, filters, and compares tandem mass spectra using matchms. Useful for searching MS/MS reference libraries, calculating spectral similarity, and building score matrices. CX Codex +1 1,900installs protocolsio-integration K-Dense-AI skill This skill reads and validates protocols.io data against the official REST contracts, and turns any change into a plan first. Useful when you need a protocol or one exact version. CX Codex +1 1,900installs scvelo K-Dense-AI skill Runs RNA velocity analysis from spliced and unspliced count matrices using scVelo. Useful for directional trajectory hypotheses alongside Scanpy workflows. CX Codex +1 1,900installs phylogenetics K-Dense-AI skill 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. CX Codex +1 1,900installs flowio K-Dense-AI skill Reads and writes flow cytometry FCS 2.0, 3.0 and 3.1 files: metadata, channels, events as NumPy. Useful when you need to look inside an FCS file or feed it to pandas. CX Codex +1 1,900installs pytdc K-Dense-AI skill Integrates Therapeutics Data Commons workflows into coding agents to discover ML datasets, plan task splits, and run molecular oracles safely. CX Codex +1 1,900installs geniml K-Dense-AI skill Checks BED and genomic-universe contracts, then plans Region2Vec and scEmbed runs. Use it before local genomic-interval analysis. CX Codex +1 1,900installs 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 +1 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 +1 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 +1 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 +1 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 +1 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 +1 1,900installs treatment-plans K-Dense-AI skill This skill formats and structurally validates local treatment-plan documentation once clinical decisions have been made and verified. It does not make clinical decisions. CX Codex +1 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 +1 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 +1 1,900installs cirq K-Dense-AI skill A skill for Google Quantum AI's Cirq framework: build and simulate quantum circuits, model noise, run on hardware. Useful when your Python project touches quantum computing. CX Codex +1 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 +1 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 +1 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 +1 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 +1 1,900installs

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