Daily repo health check — scans recent commits, CI failures, dependency drift, performance regressions, and untested code paths.
AI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.
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
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional — from…
Runs a Trailmark structural review gate over a branch, pull request, fix commit, release diff, or git ref range to detect new entrypoints, new tainted paths, removed validation or…
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H — from…
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering…
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction.
Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot.
AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.
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…
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with M — from…
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission infer — from…
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — 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…
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations.
Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immun — from…
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib.
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionarie — from…
Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality sc — from…
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis.
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
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…
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profi — from…
Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads.
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally i — from…
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing — from…
Detect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods.
De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly…
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. — from bg-szy/TOP-SKILLS
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…
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or — from…
AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.
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…
Analyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics.
Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Unified agent for leveraging single-cell foundation models (scGPT, scBERT, Geneformer, scFoundation) for cross-species annotation, perturbation prediction, and gene network…
AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and…
AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.
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…
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CAT — from…
AI-powered minimal residual disease (MRD) analysis for multiple myeloma using next-generation flow cytometry, NGS, and mass spectrometry approaches.
Performs graph-assisted triage of a single security finding, SARIF result, weAudit annotation, suspicious function, or report excerpt using Trailmark reachability, entrypoint…
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
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic struc — from…
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.
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…
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
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform d — from…
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation.
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…
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or — from…