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SkillsMP has collected 496 skills from zja2004/BGI-CLI. Open a skill to review its source and details.
zja2004/BGI-CLIShowing 40 of 496 collected skills.
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid…
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples.
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from…
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical…
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.
Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks. Provides insights on mechanisms, adaptations, interactions, and life processes. Use when: Biological systems,…
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design,…
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For…
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills…
All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding…
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in…
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level…
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for…
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties,…
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify…
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates,…
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for…
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.