Skill UI

A comprehensive toolkit for running and analyzing molecular dynamics (MD) simulations. This skill covers the entire workflow: system setup, force field definition, energy minimization, and equilibration using industry-standard tools like OpenMM and MDAnalysis. Essential for structural biology, drug binding studies, and biophysics research.

A comprehensive research toolkit for building and auditing reproducible workflows for physiological time-series data. It specializes in preprocessing, event/interval analysis, multimodal alignment, and extracting variability and complexity features from signals like ECG and EDA. Designed strictly for academic and research use, emphasizing rigorous data contracts and method-aware validation, while strictly disclaiming any diagnostic or medical device validation role.

A comprehensive end-to-end toolkit for analyzing high-density Neuropixels extracellular recordings. It guides the user through the complete electrophysiology workflow, including data loading (SpikeGLX, NWB), robust preprocessing, motion/drift correction, advanced spike sorting (Kilosort4, etc.), quality metric calculation, and AI-assisted unit curation. Ideal for generating publication-ready results from large neural datasets.

PathML is a robust computational platform engineered for local, research-only workflows in computational pathology. It facilitates comprehensive analysis pipelines, including whole slide image (WSI) loading and tiling, preprocessing, quality control (QC), quantification of multiplex images, and the construction of spatial graphs. Designed with strict adherence to data privacy and research reproducibility, it supports advanced biological data analysis.

This comprehensive toolkit facilitates the entire phylogenetic analysis workflow, from sequence alignment to tree inference. It integrates industry-standard tools like MAFFT for multiple sequence alignment, TrimAl for alignment trimming, and powerful maximum likelihood methods using IQ-TREE 2 or FastTree. Ideal for molecular genomics, tracing viral phylodynamics, studying protein evolution, or conducting molecular clock analysis. Built using Python for seamless integration.

PyOpenMS is a powerful Python library providing bindings to the OpenMS platform for comprehensive mass spectrometry data analysis. It supports end-to-end workflows in proteomics and metabolomics, including feature detection, peptide/protein identification, quantification (label-free/isobaric), and advanced data processing. Users can leverage ready-to-run scripts for tasks like format conversion, accurate mass searching, and multi-sample quantification.

A comprehensive Python toolkit built on AnnData for analyzing single-cell RNA-seq data. It supports the complete workflow, including quality control (QC), normalization, dimensionality reduction (PCA, UMAP, t-SNE), clustering, marker identification, and cell type annotation. Users benefit from a suite of ready-to-run CLI scripts that guide the entire process from raw data loading to publication-quality visualization.

A comprehensive toolkit for building, evaluating, and auditing survival models, specifically handling right-censored and competing-risk outcomes. It supports various models including Cox PH, survival forests, and SVMs, while providing best practices for leakage-safe preprocessing and robust performance evaluation in clinical or scientific ML workflows.

This skill provides end-to-end guided statistical analysis for research data, covering hypothesis testing (t-tests, ANOVA, chi-square), regression, correlation, and modern Bayesian methods. It walks users through the entire research workflow, emphasizing proper assumption checking, calculating effect sizes, conducting power analysis, and generating reports in APA format.

This comprehensive guide provides advanced workflows for interacting with ClickHouse. It covers efficient bulk data insertion (CSV, JSON), complex analytical querying (funnel analysis, retention), implementing materialized views for pre-aggregation, and utilizing powerful window functions. Ideal for building high-performance OLAP dashboards and executing large-scale data transformations.

This skill provides a comprehensive workflow for generating professional and structured financial reports. It guides the user through planning, writing, and editing various sections, and can also generate necessary chart configurations using visual tools. Ideal for condensing complex financial analysis into clear, actionable reports.

Execute comprehensive, asynchronous transcription workflows using AssemblyAI. This tool handles file upload, queues jobs, and provides advanced audio intelligence features. Capabilities include speaker diarization, sentiment analysis, named entity recognition (NER), topic categorization (IAB), content safety moderation, and sensitive PII redaction. Ideal for processing meeting recordings, interviews, and large volumes of spoken content.