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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.
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.
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.
Expert guidance for Evidence, the open-source BI framework that generates beautiful, interactive dashboards from SQL queries and Markdown. Helps developers build data reports as code, deploy them as static sites, and create self-service analytics without heavy BI tools.
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.
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your
End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.
Write clinical trial protocols with methodology. TRIGGERS - Use when user needs help with clinical-trial-protocol related tasks.
Design clinical trial site selection criteria. TRIGGERS - Use when user needs help with clinical-site-selection related tasks.
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.
Plan companion diagnostic development programs. TRIGGERS - Use when user needs help with companion-diagnostic related tasks.
Plan drug development programs with phases and timelines. TRIGGERS - Use when user needs help with drug-development-plan related tasks.
Prepare regulatory submission documents for FDA/EMA. TRIGGERS - Use when user needs help with regulatory-submission related tasks.
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