Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type pro — from…
Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling. — from bg-szy/TOP-SKILLS
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka).
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints.
Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
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 m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data. — from bg-szy/TOP-SKILLS
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts.
End-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differentia — 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
End-to-end MeRIP-seq analysis from FASTQ to m6A peaks and differential methylation. Use when analyzing epitranscriptomic m6A modifications from immunoprecipitation data.
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…
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations.
An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning.
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H — from…
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools.
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…
AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and…
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 r — from…
Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets.
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.
Write production-quality GenLayer intelligent contracts. Always pins concrete GenVM runner version hashes and never uses local-only test/latest runner aliases.
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies.
AI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.
Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query…
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio…
AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC.
Geometric deep learning-based polygenic risk score prediction using PRS-Net for modeling gene interactions, enhanced disease prediction, and cross-ancestry portability.
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 ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib.
Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction.
AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector gr — from…
AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immun — from…
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.
AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy — from…
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NC — from…
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.
Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immun — from…
AI-powered multimodal diagnostic fusion integrating radiology imaging (CT/MRI/PET), digital pathology (WSI), genomics, and clinical data for comprehensive cancer diagnosis and…