Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIA — from…
Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions.
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage…
Ultra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets — from…
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints.
An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design. — from bg-szy/TOP-SKILLS
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython.
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…
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies.
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-ng. Use when inferring publication-quality trees with model selection, ultrafast bootstrap, or partitioned…
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
Comprehensive AI-powered tumor microenvironment immune profiling integrating bulk deconvolution, single-cell analysis, and spatial transcriptomics for immunotherapy biomarker…
AI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting — from…
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.
Lightweight web fuzzing via ffuf — directory discovery, parameter testing, subdomain enumeration.
Reference for building Starknet applications using starknet.js v9.x SDK, including contract interaction, account management, transaction handling, fee estimation, wallet — from…
Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods.
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Expands one confirmed or suspected vulnerability into a Trailmark graph neighborhood of variant candidates by finding sibling functions, shared callers and callees, common…
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources — from…
AI-powered RNA velocity analysis for predicting cellular state transitions, differentiation trajectories, and dynamic gene regulation from single-cell RNA sequencing data.
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and…
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statis — from…
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
AI-powered T-cell receptor repertoire analysis for cancer diagnosis, immunotherapy response prediction, and therapeutic TCR selection using deep learning and multi-layer ML…
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X.
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival cu — from…
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any se — from…
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs.
AI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.
Analyzes medical images (X-ray, MRI, CT) using multimodal LLMs to identify anomalies and generate reports. — from bg-szy/TOP-SKILLS
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods.
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Knowledge base advisor — search, synthesize, and update your team's knowledge repositories.
Classifies genetic variants according to ACMG (American College of Medical Genetics) guidelines. — from bg-szy/TOP-SKILLS
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.
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.
Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.
Database performance audit — detects N+1 queries, missing indexes, join opportunities, slow queries, EXPLAIN analysis, and per-endpoint DB call counts.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
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. — from bg-szy/TOP-SKILLS
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels.
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…