Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs.
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs.
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating imm — from…
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating imm — from…
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools.
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools.
Clusters genes by temporal expression profile shape using Mfuzz soft clustering, TCseq, and DEGreport degPatterns.
Infers dynamic gene regulatory networks from bulk time-series expression data using Granger causality (statsmodels), dynGENIE3 (Extra-Trees on ODE-derived expression derivatives),…
Models continuous temporal trajectories from bulk or time-resolved omics data using generalized additive models (mgcv), spline regression, and changepoint detection (segmented,…
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes.
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. — from bg-szy/TOP-SKILLS
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. — from bg-szy/TOP-SKILLS
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that — from…
Call structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large…
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structu — from…
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream ana — from…
Normalize indel representation, decompose MNPs, and split multiallelic variants using bcftools norm. Use when comparing variants from different callers, preparing VCF for database…
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structu — from…
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structu — from…
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
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
Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible…
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…
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker.
End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting.
End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding.
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats…
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCa — from…
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization.
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profi — from…
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac.
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immun — from…
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission infer — from…
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visual — from…
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation — from…
End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data. — from bg-szy/TOP-SKILLS
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer — from…
Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping.
Design biodiversity strategies. TRIGGERS - Use when user needs help with biodiversity-strategy related tasks.
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to — from…
Carbon, nitrogen, phosphorus, sulfur, and water cycles — pools, fluxes, residence times, and anthropogenic perturbations.
Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.
Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.
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…
Draft `BiomarkerActionability` (BMA-*) and `Biomarker` (BIO-*) sidecar candidates for OpenOnco maintainer review from manifest-owned entities only.
Update Biome linting rules, formatting configs, and import organization settings. Use when adding new lint rules, customizing code style, or fixing workspace-specific linting…
Use when biome configuration including biome.json setup, schema versions, VCS integration, and project organization.
Execute read-only KQL queries against Kusto / Azure Data Explorer clusters via the Kusto MCP server. Read-only -- does not create, alter, or drop objects.
Execute read-only DAX queries against Power BI semantic models via the Power BI MCP server -- metadata discovery with INFO.VIEW functions and data retrieval with EVALUATE.