Data & Analytics

Data analysis, BI, visualization, datasets, statistics, and ML workflows

skills in category: 12,629
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Showing 11,185–11,208 of 12,629 skills

Scikit Image ProcessingAPython image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time video; CellPose for DL cell segmentation; napari for visualization.datapythongoVotes: 0GitHub stars: 368
Pyimagej Fiji BridgeAPython bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.datapythongoVotes: 0GitHub stars: 368
Opencv Bioimage AnalysisAComputer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++. Use scikit-image for scientific morphometry/regionprops; OpenCV for real-time, video, classical feature extraction.datapythonc++Votes: 0GitHub stars: 368
Napari Image ViewerAInteractive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows. Use ImageJ/FIJI for macro processing; napari for Python-native interactive visualization and DL segmentation review.datapythongoVotes: 0GitHub stars: 368
Flowio Flow CytometryAParse/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.datapythonbashVotes: 0GitHub stars: 368
Cellpose Cell SegmentationADL 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 watershed for rule-based; Cellpose when DL generalization across staining is needed.datapythongoVotes: 0GitHub stars: 368
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Statsmodels Statistical ModelingAPython 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.datapythongoVotes: 0GitHub stars: 368
Statistical AnalysisAGuided 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, reliability) and Bayesian. Use statsmodels or pymc-bayesian-modeling to fit.datapythongoVotes: 0GitHub stars: 368
Scikit Survival AnalysisATime-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 for frequentist, pymc for Bayesian, lifelines for parametric.datapythongoVotes: 0GitHub stars: 368
Pymc Bayesian ModelingABayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.datapythonrustVotes: 0GitHub stars: 368
Single Cell AnnotationABest practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.datapythonrustVotes: 0GitHub stars: 368
Seaborn Statistical VisualizationAStatistical 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.datapythongoVotes: 0GitHub stars: 368
Plotly Interactive VisualizationAInteractive 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 grammar use seaborn.datapythongoVotes: 0GitHub stars: 368
Opentrons IntegrationAOpentrons 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.datapythongoVotes: 0GitHub stars: 368
Tooluniverse Statistical ModelingAPerform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regression (binary/ordinal/multinomial), mixed-effects models, Cox proportional hazards survival analysis, Kaplan-Meier estimation, and comprehensive model diagnostics. Extracts odds ratios, hazard ratios, confidence intervals, p-values, and effect sizes. Designed to solve BixBench statistical reasoning questions involving clinical/experimental data. Use when asked to fit regressi...datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse Proteomics AnalysisAAnalyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and protein-protein interactions. Processes MaxQuant, Spectronaut, DIA-NN, and other MS platform outputs. Performs normalization, statistical analysis, pathway enrichment, and integration with transcriptomics. Use when analyzing proteomics data, comparing protein abundance between conditions, identifying PTM changes, studying protein complexes, integrat...datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse PhylogeneticsAProduction-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse fo...datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse Metabolomics AnalysisAAnalyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments. Performs normalization, statistical analysis, pathway enrichment, metabolite-enzyme integration, and biomarker discovery. Use when analyzing metabolomics datasets, identifying differential metabolites, studying metabolic pathways, integrating with transcriptomics/proteomics, discovering metabolic biomark...datapythonreactVotes: 0GitHub stars: 2,984
Tooluniverse Immune Repertoire AnalysisAComprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict epitope specificity. Integrate with single-cell data for clonotype-phenotype associations. Use for adaptive immune response profiling, cancer immunotherapy research, vaccine response assessment, autoimmune disease studies, or repertoire diversity analysis in immunology research.datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse Image AnalysisAProduction-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of imaging-derived measurements. Processes ImageJ/CellProfiler output (area, circularity, intensity, cell counts), performs Dunnett's test, Cohen's d effect size, power analysis, Shapiro-Wilk normality tests, two-way ANOVA, polynomial regression, natural spline regression with confidence intervals, and comparative morphomet...datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse EpigenomicsAProduction-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse ...datapythongoVotes: 0GitHub stars: 2,984
Tooluniverse Crispr Screen AnalysisAComprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets. Perform sgRNA count processing, gene-level scoring (MAGeCK, BAGEL), quality control, pathway enrichment, and drug target prioritization. Use for CRISPR screen analysis, gene essentiality studies, synthetic lethality detection, functional genomics, drug target validation, or iden...datapythongoVotes: 0GitHub stars: 2,984
Tme Immune Profiling AgentA--> --- name: 'tme-immune-profiling-agent' description: 'Comprehensive AI-powered tumor microenvironment immune profiling integrating bulk deconvolution, single-cell analysis, and spatial transcriptomics for immunotherapy biomarker discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **TME Immune Profiling Agent** provides comprehensive tumor microenvironment (TME) immune profiling by in...datapythongoVotes: 0GitHub stars: 2,984
Timesfm ForecastingAZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.datapythongoVotes: 0GitHub stars: 2,984