القائمة
جمع SkillsMP عدد ٢٤٠ من skills من AlterLab-IEU/AlterLab-Academic-Skills. افتح أي skill لمراجعة مصدره وتفاصيله.
عرض ٤٠ من أصل ٢٤٠ skills مجمعة.
The 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…
لغة النص الأصلي: الإنجليزية
Runs quantitative meta-analysis — computes effect sizes (Hedges' g / standardized mean difference, log odds/risk ratios) with their variances, pools them under fixed-effect and random-effects models, quantifies heterogeneity (I-squared, tau-squared, Cochran's…
لغة النص الأصلي: الإنجليزية
Handles missing data with principled methods — forces an explicit MCAR / MAR / MNAR mechanism statement, then applies multiple imputation by chained equations (MICE) with Rubin's-rules pooling of estimates and standard errors, or full-information maximum…
لغة النص الأصلي: الإنجليزية
Fits and reports mixed-effects / multilevel / hierarchical models for clustered, nested, longitudinal, and repeated-measures data — random intercepts and slopes, variance components and the ICC, cross-level interactions, and GLMMs (logistic/Poisson) — using…
لغة النص الأصلي: الإنجليزية
Analyzes qualitative data as a dispatched pipeline module — codebook development, thematic / framework / content analysis, and inter-coder reliability computed correctly (Krippendorff's alpha as primary via the krippendorff package or a bundled stdlib nominal…
لغة النص الأصلي: الإنجليزية
Coordinates a social-science study through the stage-gated methods pipeline — question then design-gate then measurement-gate then sampling-gate then the right analysis module then inference-gate then reporting — holding a single YAML Design Passport that…
لغة النص الأصلي: الإنجليزية
Gates trustworthiness before qualitative or interpretivist claims are written — the qualitative analog of the measurement gate. Checks that researcher positionality and role are stated, that the four Lincoln & Guba trustworthiness criteria are addressed…
لغة النص الأصلي: الإنجليزية
Analyzes complex-sample survey data with design-based inference — declares a survey design (weights, strata, PSUs/clusters, FPC) before estimating means, totals, proportions, ratios, and quantiles, computes design-adjusted standard errors via Taylor…
لغة النص الأصلي: الإنجليزية
Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD,…
لغة النص الأصلي: الإنجليزية
Query and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale…
لغة النص الأصلي: الإنجليزية
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper (methods, results, sample sizes, quality scores, conclusions). Use when running a literature review or…
لغة النص الأصلي: الإنجليزية
Builds agent-based models of social systems with Mesa 3 — the current AgentSet API (model.agents.shuffle_do('step'), auto-assigned unique_id, mandatory super().__init__(seed=...)), cell spaces (mesa.discrete_space OrthogonalMooreGrid / classic mesa.space…
لغة النص الأصلي: الإنجليزية
Estimates causal effects from observational and quasi-experimental data — difference-in-differences, instrumental variables, regression discontinuity, panel fixed effects, propensity-score / doubly-robust methods, and heterogeneous treatment effects (CATE) —…
لغة النص الأصلي: الإنجليزية
Runs Qualitative Comparative Analysis — crisp-set (csQCA), multi-value (mvQCA), and fuzzy-set (fsQCA) — for small-to-medium-N configurational research: calibrating raw data into set membership, building and refining a truth table, and Boolean minimization…
لغة النص الأصلي: الإنجليزية
Fits and evaluates measurement models — confirmatory factor analysis, full structural equation models, exploratory factor analysis, item response theory, and multi-group measurement invariance — using the verified Python stack: semopy (model syntax =~ / ~ /…
لغة النص الأصلي: الإنجليزية
Applies social-network-analysis method discipline to relational data — degree/betweenness/closeness/eigenvector centrality and PageRank, community detection (Louvain and greedy-modularity native in networkx, Leiden via igraph), and inferential network models…
لغة النص الأصلي: الإنجليزية
Routes a social-science study to its research design — true experiment, quasi-experiment (difference-in-differences, instrumental variables, regression discontinuity, interrupted time series, fixed effects), observational/correlational, qualitative, or mixed…
لغة النص الأصلي: الإنجليزية
Audits final inferential claims against the design, sample, and uncertainty before they are written or published — refuses causal language unless the design's identifying assumption is defended (else downgrades to associational), corrects p-value and…
لغة النص الأصلي: الإنجليزية
Gates measurement quality before a scale or instrument is trusted — checks that each construct is defined and operationalized, that reliability is evidenced with McDonald omega (not Cronbach alpha alone, which assumes tau-equivalence and is only a lower…
لغة النص الأصلي: الإنجليزية
Gates who is sampled, how, and how many before data collection — checks that the sampling FRAME matches the target population (coverage error), that the METHOD is named (probability vs non-probability: simple random, stratified, cluster, systematic, quota,…
لغة النص الأصلي: الإنجليزية
Analyzes text as social-science data — topic modeling (BERTopic with embeddings + class-based TF-IDF, LDA/NMF via scikit-learn or gensim), document embeddings (sentence-transformers), dictionary/lexicon methods, and supervised text classification — choosing…
لغة النص الأصلي: الإنجليزية
Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when…
لغة النص الأصلي: الإنجليزية
Apply 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. Use when annotating cell…
لغة النص الأصلي: الإنجليزية
Explore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and…
لغة النص الأصلي: الإنجليزية
Verify publication figures with a render-then-check QA pass — data-fidelity against every underlying row, axis/label floor-and-ceiling legibility, bounding-box collision detection for overlapping text/markers, and 300-dpi print-readiness. Use when proofing or…
لغة النص الأصلي: الإنجليزية
Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when…
لغة النص الأصلي: الإنجليزية
Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model…
لغة النص الأصلي: الإنجليزية
Generate 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,…
لغة النص الأصلي: الإنجليزية
Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA,…
لغة النص الأصلي: الإنجليزية
Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a…
لغة النص الأصلي: الإنجليزية
Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and…
لغة النص الأصلي: الإنجليزية
Dispatch long-running GPU/CPU jobs to remote compute with a provider-agnostic submit → poll → harvest pattern across SLURM/HPC (sbatch, squeue, sacct) and managed APIs (Modal, RunPod, GCP Batch / Vertex AI). Use when submitting a batch job to a cluster,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence,…
لغة النص الأصلي: الإنجليزية
Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
Run 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. Use when…
لغة النص الأصلي: الإنجليزية
Run 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. Use when adding directionality to…
لغة النص الأصلي: الإنجليزية
Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold…
لغة النص الأصلي: الإنجليزية
Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use…
لغة النص الأصلي: الإنجليزية