AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.
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.
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines.
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that — from…
Write production-quality GenLayer intelligent contracts. Always pins concrete GenVM runner version hashes and never uses local-only test/latest runner aliases.
Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.
AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to…
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or in — from…
Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query…
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, gener — from…
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
AI-powered analysis of tumor clonal architecture, subclonal dynamics, and evolutionary trajectories from multi-region sequencing and longitudinal liquid biopsy data.
AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.
Automates the drafting of regulatory documents (e.g., FDA CTD sections) with citation management and audit trails.
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, o — from…
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborho — from…
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data. — from bg-szy/TOP-SKILLS
Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization.
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV — from…
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools.
Structure raw clinical notes into SOAP-format summaries with explicit contradictions, missing data, and ICD-linked assessments using the provided prompt + usage script.
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immun — from…
An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.
Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data.
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
Build project documentation sites with MkDocs static site generator. USE WHEN user mentions mkdocs, documentation site, docs site, project documentation, OR wants to create,…
Create, show, and guide with ScreenCI videos in an already-initialized project by editing `.screenci.ts` files and running the Screenci workflow.
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
AI-powered genetic variant pathogenicity prediction using PopEVE deep learning model for population-aware disease variant identification and rare disease diagnosis.
AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.
Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md.
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA a — from…
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results — from…
Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction.
Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).
Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets.
Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons.
Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.
End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods. — from bg-szy/TOP-SKILLS
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome. — from bg-szy/TOP-SKILLS
Defense-in-depth security validation — multi-layered checks for OWASP Top 10, secrets, auth, crypto, and data protection.
Upgrade superskills to the latest version. Pulls from GitHub, re-runs setup, and shows the version change.
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using Genot — from…
Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies.
AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.
AI-powered analysis of patient-derived organoid (PDO) drug screening for personalized oncology treatment selection and biomarker discovery.
Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads. — from bg-szy/TOP-SKILLS
Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tabl — from…
Generates executable Python protocols for Opentrons OT-2 and Flex robots from natural language descriptions. — from bg-szy/TOP-SKILLS
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, o — from…
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.