Results for “proteomics”

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML training, tissue segmentation, or quick tile-based inspection of histopathology slides. For end-to-end computational-pathology, deep-learning model training, nucleus segmentation, or multiplexed/spatial-proteomics (CODEX, Vectra) pipelines prefer alterlab-pathml instead. Part of the AlterLab Academic Skills suite.

Process and analyze mass spectrometry data with the Matchms Python library, including importing spectra, filtering peaks, calculating similarity scores, and building reproducible analytical workflows.

Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Generate, predict, and embed protein sequences and structures using ESM3, ESMC, and ESMFold2 with local or cloud inference.

Prisma ORM expert for schema design, migrations, query optimization, relations modeling, and database operations. Use PROACTIVELY for Prisma schema issues, migration problems, query performance, relation design, or database connection issues.

Build, fit, validate, and compare Bayesian models using PyMC, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Use for writing, reviewing, debugging, testing, or diagnosing Python Bayesian models built directly with PyMC, including Model, coords/dims, Data, random variables, potentials, posterior sampling, prior/posterior predictive checks, and InferenceData output. Trigger on model geometry, shape errors, divergences, sampler choice, mutable prediction data, and probabilistic validation. Do not use for Bambi formula models, NumPyro/JAX programs, ArviZ-only analysis of existing draws, deterministic optimization, or general statistics without PyMC code.

Fit statistical models (OLS, GLM, ARIMA, mixed models) with detailed diagnostics, residuals, and inference for econometrics and time series analysis.

Applies physical principles to model biological systems, including protein folding, membrane transport, molecular forces, and neural signaling.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Build, fit, validate, and compare Bayesian models using PyMC's modern API, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.

Generates and analyzes protein sequences and structures using ESM3, ESMC, and ESMFold2, with support for local and cloud inference.

Bayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variational inference, LOO/WAIC model comparison, and posterior predictive checks. Use when fitting Bayesian or hierarchical models, estimating posteriors and credible intervals, running probabilistic inference, or comparing models with LOO/WAIC. Part of the AlterLab Academic Skills suite.

Trains, evaluates, exports, and runs inference for person re-identification models using TAO, learning discriminative embeddings for cross-camera matching.

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.

Statsmodels is Python's premier library for statistical modeling, providing tools for estimation, inference, and diagnostics across a wide range of statistical methods.

Loads and processes whole-slide pathology images, builds spatial graphs, trains deep learning models, and analyzes multiplexed immunofluorescence data across 160+ slide formats.

Econometrics skill for panel data models. Activates when the user asks about: "panel data", "fixed effects", "random effects", "Hausman test", "within estimator", "between estimator", "two-way fixed effects", "clustered standard errors panel", "FE model", "RE model", "pooled OLS", "unobserved heterogeneity", "panel regression", "first difference estimator", "entity fixed effects", "time fixed effects", "面板数据", "固定效应", "随机效应", "豪斯曼检验", "双向固定效应", "面板回归", "个体效应", "时间效应", "一阶差分"

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pathology pipelines, analyzes multiplexed or spatial-proteomics slides, or segments nuclei. For lightweight H&E slide preprocessing, tissue masking, or plain Random/Grid/Score tile extraction prefer alterlab-histolab instead. Part of the AlterLab Academic Skills suite.