Skill UI

Biopython is a robust, comprehensive toolkit for computational molecular biology written in Python. It enables users to manipulate biological sequences (DNA, RNA, protein), parse standard formats (FASTA, GenBank, PDB, etc.), and programmatically access major bioinformatics databases like NCBI via Entrez. This skill is ideal for developing complex bioinformatics pipelines, including sequence alignment, structural analysis, and phylogenetic tree construction.

DeepTools is a comprehensive command-line toolkit for processing and analyzing high-throughput sequencing data. It supports workflows for ChIP-seq, RNA-seq, ATAC-seq, and other NGS experiments. Core capabilities include converting BAM files to normalized coverage tracks (bigWig), performing quality control (QC), sample correlation analysis, and generating publication-quality visualizations, such as heatmaps and profile plots across genomic regions.

Latch is a robust Python framework designed for building, deploying, and managing complex, scalable bioinformatics workflows as serverless pipelines. It supports integrating multiple analysis tools (like Nextflow/Snakemake) and handles cloud data management (LatchFile/LatchDir) and detailed resource configuration (GPU, CPU, memory). Ideal for running large-scale analyses such as RNA-seq, AlphaFold, and single-cell analysis in a reproducible, production-ready environment.

PyDESeq2 is a robust Python implementation for conducting differential gene expression analysis on bulk RNA-seq count data. It supports complete statistical workflows, including data loading from various formats, complex multi-factor design specifications (e.g., accounting for batch effects or covariates), normalization, and performing advanced Wald tests. It is ideal for researchers transitioning R-based DESeq2 analyses into scalable Python pipelines.

A comprehensive, scalable Python toolkit designed for end-to-end single-cell RNA-seq data analysis. It supports crucial steps including quality control (QC), normalization, dimensionality reduction (PCA, UMAP, t-SNE), cell clustering, and differential gene expression analysis. The skill provides ready-to-run scripts for analyzing various formats (e.g., .h5ad, 10X, R-native) and generating publication-quality visualizations and cell type annotations.

scikit-bio is a comprehensive Python library designed for advanced bioinformatics and biological data analysis. It provides robust capabilities for sequence manipulation (DNA, RNA, Protein), performing complex sequence alignments (pairwise and multiple), constructing and analyzing phylogenetic trees, and calculating diverse ecological metrics. It is essential for microbiome analysis, evolutionary studies, and general biological data processing, supporting standard formats like FASTA, Newick, and BIOM.

scVelo is a powerful Python package designed for RNA velocity analysis using single-cell RNA-seq data. It estimates cell state transitions by modeling the kinetics of mRNA splicing—specifically using the ratio of unspliced to spliced mRNA abundances. This allows researchers to reconstruct developmental trajectories and predict cell fates, even when only snapshot data is available, making it a vital complement to standard trajectory inference tools like Scanpy.

A comprehensive Python framework utilizing deep generative models and variational inference for advanced single-cell genomics analysis. It supports the integration and analysis of diverse multi-modal data types, including single-cell RNA-seq, ATAC-seq, CITE-seq, and spatial transcriptomics. Key applications include probabilistic batch correction, cell type annotation, and multi-omics integration.

This skill provides the core mechanism for integrating Hex into external data pipelines. It enables triggering, monitoring, and managing Hex projects (e.g., via Airflow or Dagster) programmatically. Users can implement parameterized runs, execute multi-step ETL workflows sequentially, and handle status polling and error management, making it ideal for production data orchestration.

This internal agent skill automates the complex process of determining the most likely owner or team for a bug cluster. It follows a strict 6-level precedence model, starting with cached overrides, and sequentially querying sources like Service Owners, Oncall status, CODEOWNERS, recent assignees, and committers. The process includes staleness detection and confidence scoring, providing highly accurate and auditable routing recommendations for internal development triage.

This technique guides users through a rigorous two-phase research strategy. First, conduct a broad search to identify potential papers or authors. Crucially, the system instructs the user to use the extracted "author full name" as a highly specific anchor in subsequent queries. Combining the author's name with details like journal, institution, year, or biographical information ensures the most precise and reliable results, significantly narrowing down the search scope and achieving deep academic insights.

This skill provides an end-to-end, highly reproducible workflow for bulk RNA-seq differential expression analysis. It orchestrates the entire pipeline, guiding users from raw FASTQ reads through Quality Control (QC), trimming, alignment (STAR/Salmon), quantification, generating a gene-level counts matrix, and finally executing differential expression testing (pydeseq2) and pathway enrichment analysis. It is designed for robust, statistically sound, and fully documented results.