Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
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…
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving…
AI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.
Access UniProt protein database for sequences, annotations, and functional information. Use when retrieving protein data, GO terms, domain annotations, or protein-protein…
Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods.
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping — from…
An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion). — from bg-szy/TOP-SKILLS
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionarie — from…
Parse trial protocols and patient data to produce criterion-level MET/NOT/UNKNOWN determinations with evidence and gaps for clinical trial screening tasks.
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into…
Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait — from…
Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization.
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiment — from…
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assa — from…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
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
AI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.
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
Structure raw clinical notes into SOAP-format summaries with explicit contradictions, missing data, and ICD-linked assessments using the provided prompt + usage script.
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and…
AI-powered T-cell receptor repertoire analysis for cancer diagnosis, immunotherapy response prediction, and therapeutic TCR selection using deep learning and multi-layer ML…
AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.
Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files.
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H — from…
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — 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…
Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic struc — from…
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally i — from…
AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines.
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
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
Analyzes longitudinal wearable sensor data (heart rate, activity, sleep) to detect anomalies and provide personalized health insights.
Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments.
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional — from…
Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.
Knowledge base advisor — search, synthesize, and update your team's knowledge repositories.