End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy — from…
Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md.
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies…
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython.
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…
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, gener — from…
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating a — from…
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.
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.
AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.
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…
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform d — from…
AI-powered myeloproliferative neoplasm monitoring for disease progression prediction, treatment response tracking, and transformation risk assessment in PV, ET, and myelofibrosis.
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results — from…
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
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 NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcripto — from…
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any se — from…
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…
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures.
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA a — from…
Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome.
Extracts medical entities (Diseases, Medications, Procedures) from unstructured clinical text using regex and simple rules (or LLM wrappers). — from bg-szy/TOP-SKILLS
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
AI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and validation in biomedical research.
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building anno — from…
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies.
Predicts potential off-target sites for a given sgRNA sequence using mismatch analysis. — from bg-szy/TOP-SKILLS
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type pro — from…
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, o — from…
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborho — from…
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations.
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.
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
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC.
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations.
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs.
AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.
Calculates and harmonizes Tumor Mutational Burden (TMB) across platforms to predict immunotherapy response.
AI-powered multimodal fusion of radiology (CT/MRI/PET) and pathology (H&E/IHC) imaging with clinical and genomic data for comprehensive cancer diagnostics and treatment prediction.
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA e — 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
AI-powered genetic variant pathogenicity prediction using PopEVE deep learning model for population-aware disease variant identification and rare disease diagnosis.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution — from…
Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction.
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…
Comprehensive AI-powered tumor microenvironment immune profiling integrating bulk deconvolution, single-cell analysis, and spatial transcriptomics for immunotherapy biomarker…
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.
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.