全部 Agent Skills
41,263 个结果
- Alterlab PytdcAlterLab Creative Technologies LaboratoryLoads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark dataset, applying scaffold or cold-split evaluation, or sourcing labeled molecules for ADMET, toxicity, or DTI modeling.
- Alterlab Pytorch LightningAlterLab Creative Technologies LaboratoryScalable deep-learning training with PyTorch Lightning — organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, build data pipelines and callbacks, log to W&B or TensorBoard, and run distributed training (DDP, FSDP, DeepSpeed).
- Alterlab Qiime2 AmpliconAlterLab Creative Technologies LaboratoryRuns 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and…
- Alterlab RdkitAlterLab Creative Technologies LaboratoryProvides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling.
- Alterlab Research PipelineAlterLab Creative Technologies LaboratoryOrchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-revise, final integrity check, finalize), coordinating alterlab-deep-research, alterlab-paper-writer, and alterlab-paper-reviewer into a seamless 10-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates.
- Alterlab RfdiffusionAlterLab Creative Technologies LaboratoryGenerate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functional motif into a fold, designing a binder backbone to a target surface, or building symmetric assemblies; RFdiffusion…
- Alterlab Rnaseq QuantAlterLab Creative Technologies LaboratoryQuantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2.
- Alterlab RowanAlterLab Creative Technologies LaboratoryDrives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), with cloud compute and no local setup.
- Alterlab ScanpyAlterLab Creative Technologies LaboratoryRun the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting.
- Alterlab ScgptAlterLab Creative Technologies LaboratoryApply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData.
- Alterlab Scikit BioAlterLab Creative Technologies LaboratoryAnalyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity metrics (including UniFrac), ordination (PCoA), PERMANOVA statistics, and FASTA/Newick I/O. Use for microbiome and community-ecology analysis — computing diversity, distance matrices, and ordination from feature tables. Part of the AlterLab Academic Skills suite.
- Alterlab Scikit LearnAlterLab Creative Technologies LaboratoryClassical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practice reference documentation. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, feature preprocessing, or building ML pipelines.
- Alterlab Scikit SurvivalAlterLab Creative Technologies LaboratorySurvival analysis and time-to-event modeling in Python with scikit-survival. Use when working with censored survival data, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating predictions with concordance index or Brier score, handling competing risks, or implementing any time-to-event workflow. Part of the AlterLab Academic Skills suite.
- Alterlab ScveloAlterLab Creative Technologies LaboratoryRun RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes.
- Alterlab Scvi ToolsAlterLab Creative Technologies LaboratoryTrain deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome).
- Alterlab ShapAlterLab Creative Technologies LaboratoryModel interpretability and explainability with SHAP (SHapley Additive exPlanations) — feature importance and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use when explaining ML model predictions, computing feature importance, debugging models, analyzing bias or fairness, comparing models, or implementing explainable AI across tree-based models (XGBoost, LightGBM, Random Forest)…
- Alterlab SimpyAlterLab Creative Technologies LaboratoryProcess-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-based events. Use when simulating systems where entities contend for shared resources over time, such as manufacturing systems, service operations, network traffic, or logistics. Part of the AlterLab Academic Skills suite.
- Alterlab Skill FinderAlterLab Creative Technologies LaboratoryThe AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user invokes the suite without naming one, and for a multi-stage goal (or on the keyword 'alterflow', aliases 'alterresearch' / 'ultralab') it clarifies the goal with a few questions before anything runs, selects the skills the task needs, and runs a multi-agent workflow composing them (a…
- Alterlab Squidpy SpatialAlterLab Creative Technologies LaboratoryAnalyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope).
- Alterlab Stable Baselines3AlterLab Creative Technologies LaboratoryTrains single-agent reinforcement learning agents with Stable-Baselines3 — PPO, SAC, DQN, TD3, DDPG, and A2C behind a scikit-learn-like API. Use for standard single-agent RL experiments, quick prototyping, well-documented algorithm implementations on Gymnasium environments, or adding callbacks and evaluation.
- Alterlab Statistical AnalysisAlterLab Creative Technologies LaboratoryGuided statistical analysis with hypothesis-test selection, assumption checking, effect sizes, power analysis, and APA-formatted reporting using scipy.stats, statsmodels, and pingouin (Bayesian alternatives with PyMC).
- Alterlab StatsmodelsAlterLab Creative Technologies LaboratoryStatistical modeling in Python with statsmodels — OLS/WLS/GLS, GLM, discrete-choice and count models, mixed models, ARIMA/SARIMAX/VAR, with diagnostics, robust standard errors, and coefficient-level inference.
- Alterlab SympyAlterLab Creative Technologies LaboratorySymbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas.
- Alterlab Teaching DesignAlterLab Creative Technologies LaboratoryDesigns courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Biggs), and Bloom's taxonomy alignment, generating rubrics, formative and summative assessments, syllabi, lesson plans, inclusive-pedagogy guidance, and online/hybrid course architecture.