Skill UI

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

QuTiP is a Python toolbox for simulating open and closed quantum systems, offering solvers for master equations, trajectory methods, visualization, and analysis tailored to quantum research, education, and exploratory physics studies.

RDKit delivers a Python-based cheminformatics toolkit for parsing SMILES/SDF, computing descriptors, generating 2D/3D coordinates, fingerprinting, searching substructures, managing reactions, and visualizing molecules, ideal for drug discovery and computational chemistry workflows.

Scanpy is a scalable Python toolkit for single-cell RNA-seq analyses, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, and publication-ready visualization across h5ad/10X/CSV datasets.

scikit-bio provides a Python-native biological data toolkit for reading/writing FASTA/Newick files, manipulating sequences, building alignments and phylogenies, and calculating diversity metrics for microbiome and ecology workflows.

Toolkit for Python-based survival and time-to-event modeling with scikit-survival, supporting Cox models, ensemble learners, SVMs, and evaluation metrics for censored data.

Seaborn is a powerful Python library for creating publication-quality statistical graphics. It is designed for dataset-oriented plotting, making it ideal for exploratory data analysis, multivariate analysis, and visualizing complex relationships, distributions, and comparisons with minimal code. It builds upon Matplotlib, offering high-level interfaces for functions like scatterplots, heatmaps, and pair plots.

SimPy is a powerful, process-based discrete-event simulation framework written in Python. It is designed for modeling complex systems where entities interact with shared resources and time-based events occur, such as manufacturing lines, service queues, network traffic, or logistics networks. Use this skill to analyze resource contention, simulate process optimization, conduct capacity planning, and model dynamic system behaviors.

Statsmodels is a comprehensive Python library dedicated to advanced statistical modeling and econometrics. It provides tools for rigorous statistical inference, including Ordinary Least Squares (OLS), Generalized Linear Models (GLM), mixed-effects models, and time series analysis (ARIMA). Use this skill for detailed diagnostics, coefficient estimation, hypothesis testing, and producing publication-ready statistical reports in fields like econometrics and biostatistics.

Direct REST API access to UniProt for searching proteins, fetching FASTA sequences, mapping identifiers, selecting annotations, and streaming large datasets within Python workflows.

Vaex is a high-performance Python library for lazy out-of-core DataFrames that process billions of rows without RAM. Use it to analyze massive CSV/HDF5/Arrow/Parquet tables, compute fast statistics, visualize big data, and build scikit-learn pipelines.

Zarr is a Python toolkit for chunked N-D array storage with compression, sharding, and native integrations with NumPy/Dask/Xarray, ideal for parallel I/O and scalable cloud pipelines.