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Search python , found 122 results

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Polars DataFrame Analytics

K-Dense-AI/scientific-agent-skills

High-performance Python DataFrame library built on Apache Arrow. Covers expression-based API, lazy query optimization, streaming out-of-core processing, aggregations, window functions, joins, and pandas migration for ETL and analytics pipelines.

Pymoo Multi-Objective Optimization

K-Dense-AI/scientific-agent-skills

Python framework for single- and multi-objective optimization with NSGA-II/III, MOEA/D, and SPEA2. Supports constraints, ZDT/DTLZ benchmarks, Pareto front analysis, and visualization for engineering design.

PyOpenMS Mass Spectrometry

K-Dense-AI/scientific-agent-skills

Python bindings to OpenMS for computational mass spectrometry. Analyze proteomics and metabolomics LC-MS/MS data: feature detection, peptide and protein identification, label-free and isobaric quantification, adduct and accurate-mass annotation, plus ready-to-run workflow scripts.

Python Genomic File Processing

K-Dense-AI/scientific-agent-skills

A Python library for reading, querying, filtering, and writing genomic file formats including SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix data. Supports pileup, coverage analysis, indexing, and CRAM reference operations with HTSlib integration. Ideal for bioinformatics workflows requiring low-level streaming access to genomic data.

RDKit Cheminformatics Toolkit

K-Dense-AI/scientific-agent-skills

Python cheminformatics toolkit for fine-grained molecular control: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D coordinate generation, similarity, reactions, and visualization.

Scanpy Single-Cell Analysis Pipeline

K-Dense-AI/scientific-agent-skills

Scanpy is a scalable Python toolkit for single-cell RNA-seq analysis, covering quality control, normalization, dimensionality reduction, clustering, and visualization. It supports converting R formats to h5ad and includes ready-to-run CLI scripts for end-to-end workflows, making it ideal for exploratory scRNA-seq analysis and publication-quality plotting.

Scikit-Bio Bioinformatics Toolkit

K-Dense-AI/scientific-agent-skills

Python toolkit for biological data: sequence manipulation, pairwise and multiple alignment, phylogenetic trees, alpha/beta diversity and UniFrac metrics, ordination (PCoA), PERMANOVA, and FASTA/Newick/BIOM I/O for microbiome analysis.

scVelo RNA Velocity Analysis

K-Dense-AI/scientific-agent-skills

scVelo is a Python package for RNA velocity analysis in single-cell RNA-seq data. It estimates cell state transitions from unspliced/spliced mRNA dynamics, infers trajectory directions, computes latent time, and identifies driver genes to reveal cell fate decisions.

Seaborn Statistical Visualization

K-Dense-AI/scientific-agent-skills

Seaborn is a Python visualization library built on matplotlib for creating statistical graphics. It integrates with pandas for dataset-oriented plotting, offering publication-quality defaults for distributions, relationships, and categorical comparisons. Ideal for exploratory data analysis, multivariate analysis, and complex multi-panel figures. Supports various plot types like box plots, violin plots, and heatmaps.

SHAP Model Interpretability Guide

K-Dense-AI/scientific-agent-skills

This skill covers using the SHAP library to explain and audit machine learning predictions. It guides users on selecting explainers, computing feature attributions, and validating results. It includes workflows for local and global visualizations, handling multi-output models, and ensuring model behavior descriptions are accurate without implying causality. Requires Python 3.12+ and specific SHAP versions.

Statsmodels Statistical Modeling

K-Dense-AI/scientific-agent-skills

Python library skill for statistical modeling and econometrics: OLS/GLM/mixed models, discrete choice, ARIMA time series, diagnostics, residuals, and inference with coefficient tables.

Vaex Large Dataset Analysis

K-Dense-AI/scientific-agent-skills

Vaex is a high-performance Python library designed for processing and analyzing large tabular datasets that exceed available RAM. It supports out-of-core DataFrame operations, lazy evaluation, fast aggregations, and efficient visualization of big data. Ideal for working with massive CSV, HDF5, Arrow, or Parquet files, performing statistics on billions of rows, and building machine learning pipelines without memory constraints.

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