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Skills في هذا المستودع
جمع SkillsMP عدد ٢٠٧ من skills من jaechang-hits/SciAgent-Skills. افتح أي skill لمراجعة مصدره وتفاصيله.
jaechang-hits/SciAgent-Skillsعرض ٤٠ من أصل ٢٠٧ skills مجمعة.
Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.
لغة النص الأصلي: الإنجليزية
Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance. Use…
لغة النص الأصلي: الإنجليزية
Python library for healthcare ML on EHR data: process MIMIC-III/IV, eICU, OMOP-CDM; encode medical codes (ICD, ATC, NDC); build patient-level datasets; train Transformer, RETAIN, GRASP, MedBERT for mortality, drug recommendation, readmission, diagnosis…
لغة النص الأصلي: الإنجليزية
Classical ML in Python: classification, regression, clustering, dim reduction, evaluation, tuning, preprocessing pipelines. Linear models, tree ensembles, SVMs, K-Means, PCA, t-SNE. Use PyTorch/TF for deep learning; XGBoost/LightGBM for scale.
لغة النص الأصلي: الإنجليزية
Model interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kernel, Gradient, Permutation), feature attribution, and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use to explain ML predictions,…
لغة النص الأصلي: الإنجليزية
Guidelines for clinical decision support (CDS) documents: biomarker-stratified cohort analyses and GRADE-graded treatment reports. Covers structure, executive summaries, evidence grading (1A–2C), stats (HR, CI, survival), and biomarker integration. Use for…
لغة النص الأصلي: الإنجليزية
Structured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms, design experiments. Follows the scientific method. Use scientific-brainstorming for open ideation; hypogenic for automated LLM hypothesis…
لغة النص الأصلي: الإنجليزية
Opentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker, magnetic, temperature modules. Use pylabrobot for multi-vendor.
لغة النص الأصلي: الإنجليزية
Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (DataFrame) and Graph Objects (fine control). For static publication figures use matplotlib; for statistical…
لغة النص الأصلي: الإنجليزية
Statistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter, line), categorical, regression, correlation heatmaps. Auto aggregation/CIs. Use plotly for interactive; matplotlib for low-level.
لغة النص الأصلي: الإنجليزية
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
لغة النص الأصلي: الإنجليزية
Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap,…
لغة النص الأصلي: الإنجليزية
Benchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation. Needs Benchling account and API key. Use biopython for local sequence analysis; pubchem for chemical DBs.
لغة النص الأصلي: الإنجليزية
protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing. Public access free; auth needed for private or publishing. Pair with…
لغة النص الأصلي: الإنجليزية
Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generators, I/O (GraphML, GML, edge list), matplotlib viz. For large graphs (100K+ nodes) use igraph or graph-tool; for…
لغة النص الأصلي: الإنجليزية
Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA for conferences. Includes templates. For figure generation use matplotlib-scientific-plotting or…
لغة النص الأصلي: الإنجليزية
Scientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA/ARRIVE), writing principles (clarity/conciseness/accuracy), venue-specific style. For LaTeX see companion assets.
لغة النص الأصلي: الإنجليزية
Scientific presentations for conferences, seminars, thesis defenses, and grant pitches. Slide design, talk structure, timing, data viz for slides, QA. PowerPoint and LaTeX Beamer. For posters use latex-research-posters.
لغة النص الأصلي: الإنجليزية
Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS,…
لغة النص الأصلي: الإنجليزية
Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations. Quirks: compound input_item rejects `name` (use pubchem_cid/kegg_id/inchi_key/etc.);…
لغة النص الأصلي: الإنجليزية
Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which…
لغة النص الأصلي: الإنجليزية
Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search…
لغة النص الأصلي: الإنجليزية
Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed…
لغة النص الأصلي: الإنجليزية
Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug…
لغة النص الأصلي: الإنجليزية
Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For…
لغة النص الأصلي: الإنجليزية
Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth. Always resolve…
لغة النص الأصلي: الإنجليزية
Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use…
لغة النص الأصلي: الإنجليزية
Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from…
لغة النص الأصلي: الإنجليزية
Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related…
لغة النص الأصلي: الإنجليزية
Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods.
لغة النص الأصلي: الإنجليزية
Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments
لغة النص الأصلي: الإنجليزية
Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection.
لغة النص الأصلي: الإنجليزية
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
لغة النص الأصلي: الإنجليزية
Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. Covers PICO framework for clinical questions, three-tiered search (database-specific, AI-assisted, content extraction), PubMed field tags…
لغة النص الأصلي: الإنجليزية
Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
لغة النص الأصلي: الإنجليزية
Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible. Use statsmodels…
لغة النص الأصلي: الإنجليزية
Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count,…
لغة النص الأصلي: الإنجليزية
Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.
لغة النص الأصلي: الإنجليزية
DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image…
لغة النص الأصلي: الإنجليزية
Parse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS export. Use FlowKit for gating/compensation.
لغة النص الأصلي: الإنجليزية