Bioinformatics & Life Sciences Bundle

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Included Skills (8)

1. Scarf Single Cell — Analyze single-cell RNA-seq at million-cell scale with Scarf: out-of-core Zarr stores on disk or object storage, provenance-tracked artifacts, audited QC, clustering, markers and donor comparisons.
2. Scanpy — Scanpy is a scalable Python toolkit that analyzes single-cell RNA‑seq data using the AnnData framework. It supports end‑to‑end workflows, including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Researchers and bioinformaticians use Scanpy to extract biological insights from complex single‑cell datasets.
3. Uniprot Database — The Uniprot Database skill offers direct REST API access to UniProt, enabling protein searches, FASTA retrieval, and ID mapping across Swiss-Prot and TrEMBL. It integrates seamlessly into Python workflows, providing a unified interface to multiple databases while allowing specialized control for UniProt-specific tasks. Researchers and bioinformaticians benefit from streamlined data retrieval and efficient cross-referencing within their analytical pipelines.
4. Biopython — Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
5. Genomic Intelligence — Genomic Intelligence predicts regulatory features, gene structure, and expression directly from DNA sequence using hosted transformer models, eliminating the need for local GPUs or model weights. It offers six REST‑API tasks—promoter, splice sites, enhancer activity, chromatin state, sequence‑to‑expression, and de‑novo gene annotation—plus a composite workflow that finds genes and predicts expression. Researchers and bioinformaticians can provide a gene symbol, genomic region, or FASTA sequence to obtain precise predictions via api.genomicintelligence.ai or mcp.genomicintelligence.ai.
6. Primer Design — The skill designs and audits PCR and RT‑qPCR primers using Primer3, applying thermodynamic constraints and reference‑based off‑target searches to generate traceable sequence coordinates. Researchers benefit from accurate primer pair design, validation of existing primers, and specialized applications such as exon‑junction assays or variant masking. The output clearly separates computational candidates from experimentally validated results, ensuring reliable primer selection for downstream experiments.
7. Julia Pro — Master Julia 1.10+ with modern features, performance optimization, multiple dispatch, and production-ready practices.
8. Qiime2 Amplicon — The Qiime2 Amplicon skill transforms paired‑end 16S amplicon reads into QIIME 2 ASVs, assigns taxonomy, and preserves artifact provenance while validating FASTQ manifests, primer orientation, overlap, sample IDs, runtime versions, and read retention. It recommends compatible taxonomic classifiers to ensure accurate classification. Researchers and bioinformaticians use it to generate reliable, reproducible microbiome profiles.