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End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.
A unified interface for annotating single-cell RNA-seq data using Marker Genes, Deep Learning (CellTypist), or LLMs.
Analyze DNA, RNA, and protein sequences with alignment, variant calling, and expression analysis pipelines.
Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.
Virtual gene knockout simulation using foundation models to predict transcriptional
Comprehensive scientific research toolkit with 139 specialized skills for biology, chemistry, medicine, data science, and computational research. Transforms Claude into an AI research assistant with access to scientific databases, analysis tools, and domain-specific workflows.
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopytho...
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl ...
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed ...
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting exp...
Bridge layer connecting Vertex AI / Google Cloud to plurigrid/asi protein-scale biology skills. Wires AlphaFold, ESM, DiffDock, DeepChem, and TorchDrug into Vertex AI Pipelines, Endpoints, and BigQuery genomics for protein design-predict-validate loops.
Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
Search for similar protein sequences in UniProt Swiss-Prot database using BLAST to identify homologous proteins and functional relationships.
Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.
MaxQuant mass spectrometry skill for protein identification and quantification
IGV integration skill for interactive genome visualization and review
Gene Set Enrichment Analysis skill for functional annotation and pathway interpretation
MetaPhlAn metagenomic profiling skill for species-level community composition
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