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Use when you need to connect to the SciGraph SCP server for PertKGE (knowledge graph for compound-protein interaction inference using perturbation transcriptomics + regulatory network; cold-start CPI prediction) and call its MCP tools (query_cypher, get_kg_statistics, get_entity_details, get_expe...
Use when you need to connect to the SciGraph SCP server for Otter-UBC (IBM Research Otter-Knowledge multimodal knowledge graphs for drug discovery) and call its MCP tools (query_cypher, get_kg_statistics, get_entity_details, get_experiment_workflow), including streamableHttp configuration with SC...
Use when you need to connect to the SciGraph SCP server for MiKG (microbiota–gut–brain axis biomedical knowledge graph) and call its MCP tools (query_cypher, get_kg_statistics, get_entity_details, get_experiment_workflow), including streamableHttp configuration with SCP-HUB-API-KEY and Python 3.1...
Use when you need to connect to the SciGraph SCP server for PyBioMart (Pythonic interface for querying BioMart/Ensembl; supports genomic data extraction for biomedical knowledge graphs and disease-gene association prediction via KG embeddings) and call its MCP tools (query_cypher, get_kg_statisti...
Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".
Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE coordinates and plots for group separation assessment. NOT for: differential expression testing, single-cell workflows requiring...
Generates complete non-tumor biomedical machine learning research designs from a user-provided research direction. Always use this skill when users want to plan bioinformatics + ML papers for non-cancer diseases (metabolic, cardiovascular, kidney, inflammatory, autoimmune, infectious, neurologica...
Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary graph databases, multi-omics integrati...
Generates complete network toxicology + molecular docking research designs from a user-provided toxicant and disease/phenotype. Always use this skill when users want to investigate how an environmental toxicant, endocrine disruptor, heavy metal, food contaminant, pharmaceutical residue, or consum...
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when creating publication figures of genomic regions with multiple data tracks.
AI-powered genetic variant pathogenicity prediction using PopEVE deep learning model for population-aware disease variant identification and rare disease diagnosis.
AI-powered PROTAC (Proteolysis Targeting Chimera) design for targeted protein degradation, integrating ternary complex prediction, linker optimization, and ADMET modeling.
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data f...
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
PubMed Database workflow skill. Use this skill when the user needs Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API impleme...
Biopython: Computational Molecular Biology in Python workflow skill. Use this skill when the user needs 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 bioinfor...
Scanpy: Single-Cell Analysis workflow skill. Use this skill when the user needs Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clu...
ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, f...
Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
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