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SkillsMP ha recopilado 207 skills de jaechang-hits/SciAgent-Skills. Abre una skill para revisar su origen y sus detalles.
jaechang-hits/SciAgent-SkillsMostrando 40 de 207 skills recopiladas.
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.
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
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.);…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods.
Idioma del texto original: inglés
Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments
Idioma del texto original: inglés
Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection.
Idioma del texto original: inglés
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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,…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés
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…
Idioma del texto original: inglés
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.
Idioma del texto original: inglés