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Found 86 Skills
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
Use when designing software architecture for bioinformatics pipelines, defining data structures, planning scalability, or making technical design decisions for complex systems.
Library for bioinformatics and community ecology statistics. Provides data structures and algorithms for sequences, alignments, phylogenetics, and diversity analysis. Essential for microbiome research and ecological data science. Use for alpha/beta diversity metrics, ordination (PCoA), phylogenetic trees, sequence manipulation (DNA/RNA/Protein), distance matrices, PERMANOVA, and community ecology analysis.
Use when implementing data analysis pipelines, statistical tests, or bioinformatics workflows in code (Python/R), particularly for genomics, transcriptomics, proteomics, or other -omics data.
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
Python bioinformatics library for sequence manipulation, alignments, phylogenetics, diversity metrics (Shannon, UniFrac), ordination (PCoA, CCA), statistical tests (PERMANOVA, Mantel), and biological file format I/O.
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.
Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology
Comprehensive guide for Biopython - the premier Python library for computational biology and bioinformatics. Use for DNA/RNA/protein sequence analysis, file I/O (FASTA, FASTQ, GenBank, PDB), sequence alignment, BLAST searches, phylogenetic analysis, structure analysis, and NCBI database access.
Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs. Use when a task needs quick bioinformatics lookup across genomic reference databases with the gget CLI or Python package.